From cacd2c13a719157d3a6ef0955995abdcfea194a0 Mon Sep 17 00:00:00 2001
From: Daniel Weindl <daniel.weindl@uni-bonn.de>
Date: Wed, 21 Oct 2026 20:51:45 +0200
Subject: [PATCH] Don't fail `petablint` for PEtab v2 problems with only
 warnings

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

Closes #567.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
---
 CHANGELOG.md          |  3 +++
 petab/petablint.py    |  6 +++---
 tests/v2/test_core.py | 29 +++++++++++++++++++++++++++++
 3 files changed, 35 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0e818060..e13a4fa4 100644
--- a/CHANGELOG.md
+++ b/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`
diff --git a/petab/petablint.py b/petab/petablint.py
index 6ff52826..b5260d19 100755
--- a/petab/petablint.py
+++ b/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)
diff --git a/tests/v2/test_core.py b/tests/v2/test_core.py
index 5f95ed15..f1975cd2 100644
--- a/tests/v2/test_core.py
+++ b/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."""