Interpret findings¶
Every issue carries a stable rule code, severity, category, AnnData location, message, optional evidence, remediation, and check name.
Severity¶
| Severity | Normal mode | Strict mode |
|---|---|---|
error |
Fails the report | Fails the report |
warning |
Does not fail | Fails the report |
information |
Does not fail | Does not fail |
Status¶
report.status is "pass" or "fail" after all checks run. Exit code 1
maps to a failed report; exit code 2 means validation never completed.
Reading common categories¶
| Category | Typical meaning |
|---|---|
| Identifiers | Missing or incomplete plate/well/site/cell/perturbation fields |
| Annotations | Control/treatment labels incomplete |
| Features | Compartment or measurement-family naming gaps |
| Matrix / slots | Shape, numeric validity, layer/obsm alignment |
| Metadata / provenance | Licence, schema id, image/segmentation/feature provenance |
| Aggregation | Missing or incomplete aggregation blocks on well/treatment data |
| AI readiness | Constant or heavily missing features (sampled on large matrices) |
| Profile | Declared vs detected level mismatch or ambiguity |
For fixture-derived baselines and “is this a false positive?” guidance, see Expected findings and false positives. The full code list is in the Rule catalogue.
What findings are not¶
A validation finding is not a security vulnerability and is not a biological claim. See Scientific boundaries and Security.