Found reviewing PR #345, which added data/isolates/** to the workflow's trigger paths.
scripts/validate_strict.py has DEFAULT_ROOTS = [_REPO_ROOT / "kb" / "communities"], and the workflow runs just validate-strict with no arguments. The same is true of validate-all, validate-terms-all, validate-references-all and the network auditor.
So editing an isolate now re-runs a suite whose only isolate coverage is the new test_isolates_pass_schema_validation. The trigger is right; the job behind it is still kb/communities-only.
Measured: all 4 isolates fail linkml-term-validator --labels today — GO:0055065, NCBITaxon:32207, CHEBI:46727, GO:0006118. Pre-existing and outside PR #345's scope, but it means "isolates are now gated" is true only for schema validation.
Fix: give the validation scripts a roots list covering every id-bearing directory, or state explicitly that isolates get schema validation only.
Found reviewing PR #345, which added
data/isolates/**to the workflow's trigger paths.scripts/validate_strict.pyhasDEFAULT_ROOTS = [_REPO_ROOT / "kb" / "communities"], and the workflow runsjust validate-strictwith no arguments. The same is true ofvalidate-all,validate-terms-all,validate-references-alland the network auditor.So editing an isolate now re-runs a suite whose only isolate coverage is the new
test_isolates_pass_schema_validation. The trigger is right; the job behind it is stillkb/communities-only.Measured: all 4 isolates fail
linkml-term-validator --labelstoday —GO:0055065,NCBITaxon:32207,CHEBI:46727,GO:0006118. Pre-existing and outside PR #345's scope, but it means "isolates are now gated" is true only for schema validation.Fix: give the validation scripts a roots list covering every id-bearing directory, or state explicitly that isolates get schema validation only.