petablint fails for PEtab v2 problems with only warnings #567

For PEtab v2 problems, petablint exits with 1 if lint_problem returns any issues, including warnings (petab/petablint.py, if validation_issues: ... sys.exit(1)). For PEtab v1, only errors make it fail.

For example, unused conditions are allowed by the specification, and CheckUnusedConditions reports them as WARNING, but petablint still fails:

$ petablint problem.yaml; echo $?
WARNING: Conditions {'pred2', 'pred3', 'pred4', 'pred5'} are not used in the experiments table. [CheckUnusedConditions]
1

(Giordano_Nature2020 from the benchmark collection converted with petab1to2; same for Fujita_SciSignal2010.)

This makes petablint unusable for CI checks of valid v2 problems. Suggested fix: always log the issues, but exit with 1 only if validation_issues.has_errors(). If failing on warnings is wanted, it could be an opt-in flag.

🤖 Generated by an AI agent (Claude Code)