Don't fail petablint for PEtab v2 problems with only warnings (#569)

For PEtab v2 problems, `petablint` exited with 1 for any validation
issue, including warnings such as unused conditions. Now it reports all
issues but only fails if there are errors, consistent with PEtab v1.

Use `petablint --fail-on-warnings` to get the previous behavior. This
option currently only affects PEtab v2 problems.

Closes #567.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>

Author: dweindl

CHANGELOG.md

@@ -59,6 +59,11 @@
   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.
+  The previous behavior can be restored via `--fail-on-warnings`
+  (currently only effective for PEtab v2)
+  (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/569)
 * Several fixes to `assignments_to_experiments`: keep a switch at the start
   of a later period, keep the condition changes of symbols that the model
   still uses elsewhere, evaluate a condition change once at the start of its

petab/petablint.py

@@ -53,6 +53,14 @@ def parse_cli_args():
         action="store_true",
         help="More verbose output",
     )
+    parser.add_argument(
+        "--fail-on-warnings",
+        dest="fail_on_warnings",
+        action="store_true",
+        help="Exit with a non-zero status also if there are only warnings. "
+        "Currently only supported for PEtab v2 problems; "
+        "has no effect for PEtab v1.",
+    )
 
     # Call with set of files
     group = parser.add_argument_group(
@@ -194,13 +202,24 @@ def main():
                 ret = petab.lint.lint_problem(problem)
                 sys.exit(ret)
             case 2:
-                from petab.v2.lint import lint_problem
+                from petab.v2.lint import (
+                    ValidationIssueSeverity,
+                    lint_problem,
+                )
 
+                fail_level = (
+                    ValidationIssueSeverity.WARNING
+                    if args.fail_on_warnings
+                    else ValidationIssueSeverity.ERROR
+                )
                 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 any(
+                        issue.level >= fail_level
+                        for issue in validation_issues
+                    ):
                         sys.exit(1)
                     logger.info("PEtab format check completed successfully.")
                     sys.exit(0)

tests/v2/test_core.py

@@ -1052,6 +1052,48 @@ 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
+
+    # ... unless requested
+    result = subprocess.run(  # noqa S607
+        [  # noqa: S607
+            "petablint",
+            "--fail-on-warnings",
+            str(Path(tmpdir, "problem.yaml")),
+        ],
+        capture_output=True,
+        text=True,
+    )
+    assert result.returncode == 1
+    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."""