{"version": "2.1.0", "$schema": "https://json.schemastore.org/sarif-2.1.0.json", "runs": [{"tool": {"driver": {"name": "Repobility", "informationUri": "https://repobility.com", "rules": [{"id": "scanner-d8432a00761e2b62", "name": "Possibly dead Python function: loss_fn", "shortDescription": {"text": "Possibly dead Python function: loss_fn"}, "fullDescription": {"text": "No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler."}, "properties": {"scanner": "scanner-primary", "layer": "software", "severity": "low", "confidence": 1.0}}, {"id": "scanner-a6196e084f8368c7", "name": "Possibly dead Python function: loss_fn", "shortDescription": {"text": "Possibly dead Python function: loss_fn"}, "fullDescription": {"text": "No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler."}, "properties": {"scanner": "scanner-primary", "layer": "software", "severity": "low", "confidence": 1.0}}, {"id": "scanner-e3c5368133fea6d1", "name": "Possibly dead Python function: step_extract", "shortDescription": {"text": "Possibly dead Python function: step_extract"}, "fullDescription": {"text": "No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler."}, "properties": {"scanner": "scanner-primary", "layer": "software", "severity": "low", "confidence": 1.0}}, {"id": "scanner-1d442f63b1ab14b8", "name": "Possibly dead Python function: step_embed", "shortDescription": {"text": "Possibly dead Python function: step_embed"}, "fullDescription": {"text": "No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler."}, "properties": {"scanner": "scanner-primary", "layer": "software", "severity": "low", "confidence": 1.0}}, {"id": "scanner-ae1441330c5c324e", "name": "Possibly dead Python function: step_plot", "shortDescription": {"text": "Possibly dead Python function: step_plot"}, "fullDescription": {"text": "No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler."}, "properties": {"scanner": "scanner-primary", "layer": "software", "severity": "low", "confidence": 1.0}}, {"id": "scanner-354cd3fe2e96833e", "name": "Possibly dead Python function: compute_cluster_metrics_both_spaces", "shortDescription": {"text": "Possibly dead Python function: compute_cluster_metrics_both_spaces"}, "fullDescription": {"text": "No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler."}, "properties": {"scanner": "scanner-primary", "layer": "software", "severity": "low", "confidence": 1.0}}, {"id": "scanner-37005ec46406f1b9", "name": "Possibly dead Python function: compute_hog_centroids", "shortDescription": {"text": "Possibly dead Python function: compute_hog_centroids"}, "fullDescription": {"text": "No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler."}, "properties": {"scanner": "scanner-primary", "layer": "software", "severity": "low", "confidence": 1.0}}, {"id": "scanner-ce6c55eaa12e0c1d", "name": "Possibly dead Python function: compute_silhouette_in_original_space", "shortDescription": {"text": "Possibly dead Python function: compute_silhouette_in_original_space"}, "fullDescription": {"text": "No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler."}, "properties": {"scanner": "scanner-primary", "layer": "software", "severity": "low", "confidence": 1.0}}, {"id": "scanner-083ac8ccaeb73c75", "name": "Possibly dead Python function: normalize_label", "shortDescription": {"text": "Possibly dead Python function: normalize_label"}, "fullDescription": {"text": "No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler."}, "properties": {"scanner": "scanner-primary", "layer": "software", "severity": "low", "confidence": 1.0}}, {"id": "scanner-f4dd0108b0026540", "name": "Privileged port 10 in use", "shortDescription": {"text": "Privileged port 10 in use"}, "fullDescription": {"text": "Port 10 is privileged (<1024). Make sure the service runs with the right caps or front it with a non-privileged port via a load balancer."}, "properties": {"scanner": "scanner-primary", "layer": "network", "severity": "medium", "confidence": 1.0}}, {"id": "scanner-62502203c2b4cc9f", "name": "Privileged port 11 in use", "shortDescription": {"text": "Privileged port 11 in use"}, "fullDescription": {"text": "Port 11 is privileged (<1024). Make sure the service runs with the right caps or front it with a non-privileged port via a load balancer."}, "properties": {"scanner": "scanner-primary", "layer": "network", "severity": "medium", "confidence": 1.0}}, {"id": "scanner-ae2b41fb3a1c87aa", "name": "Privileged port 60 in use", "shortDescription": {"text": "Privileged port 60 in use"}, "fullDescription": {"text": "Port 60 is privileged (<1024). Make sure the service runs with the right caps or front it with a non-privileged port via a load balancer."}, "properties": {"scanner": "scanner-primary", "layer": "network", "severity": "medium", "confidence": 1.0}}, {"id": "scanner-a8088a874e539281", "name": "Dockerfile runs as root: infra/github-runner/Dockerfile", "shortDescription": {"text": "Dockerfile runs as root: infra/github-runner/Dockerfile"}, "fullDescription": {"text": "No non-root USER set. Containers running as root expand the blast radius of any vulnerability inside the image."}, "properties": {"scanner": "scanner-primary", "layer": "hardware", "severity": "medium", "confidence": 1.0}}, {"id": "scanner-52e52cb8bd0219d6", "name": "Docker base image is tag-pinned but not digest-pinned: ubuntu:24.04", "shortDescription": {"text": "Docker base image is tag-pinned but not digest-pinned: ubuntu:24.04"}, "fullDescription": {"text": "Container tags can be retagged upstream. Pin production base images to a reviewed digest (`image@sha256:...`) when reproducibility and supply-chain integrity matter."}, "properties": {"scanner": "scanner-primary", "layer": "hardware", "severity": "low", "confidence": 1.0}}, {"id": "scanner-18dc3fa21bb6af0b", "name": "Insecure pattern 'direct_innerhtml_assignment' in chapters/chapter2/hog_umap_interactive.py:360", "shortDescription": {"text": "Insecure pattern 'direct_innerhtml_assignment' in chapters/chapter2/hog_umap_interactive.py:360"}, "fullDescription": {"text": "Found a known-risky pattern (direct_innerhtml_assignment). Review and replace if possible."}, "properties": {"scanner": "scanner-primary", "layer": "security", "severity": "medium", "confidence": 1.0}}, {"id": "scanner-6372cebde0220094", "name": "No auth library detected", "shortDescription": {"text": "No auth library detected"}, "fullDescription": {"text": "The scanner did not find any standard auth library (JWT, OAuth, NextAuth, Auth0, etc.). The repo has auth/admin/session surface indicators, so auth may live in custom code, in a separate service, or be missing."}, "properties": {"scanner": "scanner-primary", "layer": "security", "severity": "medium", "confidence": 1.0}}, {"id": "scanner-a2483bc396beed6d", "name": "GitHub Action is tag-pinned rather than SHA-pinned", "shortDescription": {"text": "GitHub Action is tag-pinned rather than SHA-pinned"}, "fullDescription": {"text": "actions/checkout@v4 can move without a code change in this repo. Pin third-party actions to a reviewed 40-character commit SHA."}, "properties": {"scanner": "scanner-primary", "layer": "cicd", "severity": "low", "confidence": 1.0}}, {"id": "scanner-6893a6c8b0861585", "name": "Very low test-to-source ratio", "shortDescription": {"text": "Very low test-to-source ratio"}, "fullDescription": {"text": "0 test file(s) for 41 source file(s) (ratio 0.00). Consider adding integration or unit tests for critical paths."}, "properties": {"scanner": "scanner-primary", "layer": "quality", "severity": "medium", "confidence": 1.0}}, {"id": "scanner-141b30a41e03817b", "name": "No license file detected", "shortDescription": {"text": "No license file detected"}, "fullDescription": {"text": "No LICENSE/COPYING/NOTICE file was found. Generated repositories often omit licensing, which blocks reuse and automated intake."}, "properties": {"scanner": "scanner-primary", "layer": "quality", "severity": "low", "confidence": 1.0}}, {"id": "scanner-3ab5d313dda8e5f9", "name": "Debug logging residue appears in source files", "shortDescription": {"text": "Debug logging residue appears in source files"}, "fullDescription": {"text": "Found 772 console/debugger/print-style debug statements in non-test source. This is a common fast-generation residue before production cleanup."}, "properties": {"scanner": "scanner-primary", "layer": "quality", "severity": "low", "confidence": 1.0}}, {"id": "scanner-11825279136b53a3", "name": "CI is configured but no tests are detected", "shortDescription": {"text": "CI is configured but no tests are detected"}, "fullDescription": {"text": "A CI pipeline exists, but the scan found no test files to gate. Opus labeled this generated-code pattern as config theater: release machinery exists, but it has little behavioral signal."}, "properties": {"scanner": "scanner-primary", "layer": "quality", "severity": "medium", "confidence": 1.0}}, {"id": "scanner-b9088664ace7f748", "name": "Composite production-readiness gap", "shortDescription": {"text": "Composite production-readiness gap"}, "fullDescription": {"text": "Multiple low-cost hardening controls are missing together: license, tests. Opus verification showed these co-occurring gaps are a better readiness signal than reading each flag in isolation."}, "properties": {"scanner": "scanner-primary", "layer": "quality", "severity": "low", "confidence": 1.0}}, {"id": "scanner-749d4bc1bd66df5f", "name": "Agent instructions exist but release-hardening basics are missing", "shortDescription": {"text": "Agent instructions exist but release-hardening basics are missing"}, "fullDescription": {"text": "AI-coder instruction files were found, but the repo is missing license, tests. Treat this as a contract gap: the agent is guided, but the generated output is not yet guarded by the controls that make it repeatable."}, "properties": {"scanner": "scanner-primary", "layer": "quality", "severity": "medium", "confidence": 1.0}}, {"id": "scanner-2679282aa1c484b5", "name": "Agent authority lacks a verifier contract: AGENTS.md", "shortDescription": {"text": "Agent authority lacks a verifier contract: AGENTS.md"}, "fullDescription": {"text": "This agent instruction grants code or shell authority but does not state the verification gate that decides promotion. The recurring safe pattern is: LLM proposes; deterministic tests/build/security checks verify; only verified code promotes."}, "properties": {"scanner": "scanner-primary", "layer": "quality", "severity": "medium", "confidence": 1.0}}, {"id": "scanner-62145700491acf94", "name": "Agent authority lacks a verifier contract: .claude/skills/orchestrate/SKILL.md", "shortDescription": {"text": "Agent authority lacks a verifier contract: .claude/skills/orchestrate/SKILL.md"}, "fullDescription": {"text": "This agent instruction grants code or shell authority but does not state the verification gate that decides promotion. The recurring safe pattern is: LLM proposes; deterministic tests/build/security checks verify; only verified code promotes."}, "properties": {"scanner": "scanner-primary", "layer": "quality", "severity": "medium", "confidence": 1.0}}, {"id": "scanner-33c066fd835c73b8", "name": "Network/subprocess call without timeout or try/except \u2014 write_artifact_metadata.py:31", "shortDescription": {"text": "Network/subprocess call without timeout or try/except \u2014 write_artifact_metadata.py:31"}, "fullDescription": {"text": "`subprocess.run(...)` here lacks both a `timeout=` arg and an enclosing try/except. This is exactly the class of bug that took down our git-clone earlier (HTTP/2 stream cancel surfaced as a fatal). Add a `timeout=` and wrap in try/except, or use a wrapper that retries."}, "properties": {"scanner": "scanner-primary", "layer": "quality", "severity": "medium", "confidence": 1.0}}, {"id": "scanner-e085cdb333e5da1a", "name": "Network/subprocess call without timeout or try/except \u2014 chapters/chapter2/run.py:117", "shortDescription": {"text": "Network/subprocess call without timeout or try/except \u2014 chapters/chapter2/run.py:117"}, "fullDescription": {"text": "`subprocess.run(...)` here lacks both a `timeout=` arg and an enclosing try/except. This is exactly the class of bug that took down our git-clone earlier (HTTP/2 stream cancel surfaced as a fatal). Add a `timeout=` and wrap in try/except, or use a wrapper that retries."}, "properties": {"scanner": "scanner-primary", "layer": "quality", "severity": "medium", "confidence": 1.0}}, {"id": "scanner-2c04133e54348533", "name": "Near-duplicate function bodies in 2 places", "shortDescription": {"text": "Near-duplicate function bodies in 2 places"}, "fullDescription": {"text": "Functions with the same first-5-line body hash:\nchapters/chapter2/02_build_dataset.py:load_sequences, chapters/chapter2/archive/scripts/build_cafa3_dataset.py:load_sequences\n\nThis is *the* AI-coder failure mode (4\u00d7 more duplication in vibe-coded repos \u2014 see https://jw.hn/ai-code-hygiene). Consolidate or document why they're separate."}, "properties": {"scanner": "scanner-primary", "layer": "quality", "severity": "low", "confidence": 1.0}}]}}, "automationDetails": {"id": "repobility/23881"}, "properties": {"repository": "acefesan/dl-bio", "repoUrl": "https://github.com/acefesan/dl-bio", "branch": "main"}, "results": [{"ruleId": "scanner-d8432a00761e2b62", "level": "note", "message": {"text": "Possibly dead Python function: loss_fn"}, "properties": {"repobilityId": "6e2b105b0c705a4b", "scanner": "scanner-primary", "fingerprint": "d8432a00761e2b62", "layer": "software", "severity": "low", "confidence": 1.0, "tags": ["dead-code"]}, "locations": [{"physicalLocation": {"artifactLocation": {"uri": "chapters/chapter2/05_go_prediction.py:119"}, "region": {"startLine": 1}}}]}, {"ruleId": "scanner-a6196e084f8368c7", "level": "note", "message": {"text": "Possibly dead Python function: loss_fn"}, "properties": {"repobilityId": "6e2b105b0c705a4b", "scanner": "scanner-primary", "fingerprint": "a6196e084f8368c7", "layer": "software", "severity": "low", "confidence": 1.0, "tags": ["dead-code"]}, "locations": [{"physicalLocation": {"artifactLocation": {"uri": "chapters/chapter2/06_go_grid_search.py:111"}, "region": {"startLine": 1}}}]}, {"ruleId": "scanner-e3c5368133fea6d1", "level": "note", "message": {"text": "Possibly dead Python function: step_extract"}, "properties": {"repobilityId": "3cff0d51a4b8cbdd", "scanner": "scanner-primary", "fingerprint": "e3c5368133fea6d1", "layer": "software", "severity": "low", "confidence": 1.0, "tags": ["dead-code"]}, "locations": [{"physicalLocation": {"artifactLocation": {"uri": "chapters/chapter2/hog_umap.py:76"}, "region": {"startLine": 1}}}]}, {"ruleId": "scanner-1d442f63b1ab14b8", "level": "note", "message": {"text": "Possibly dead Python function: step_embed"}, "properties": {"repobilityId": "9a7d6ac4f8a4b105", "scanner": "scanner-primary", "fingerprint": "1d442f63b1ab14b8", "layer": "software", "severity": "low", "confidence": 1.0, "tags": ["dead-code"]}, "locations": [{"physicalLocation": {"artifactLocation": {"uri": "chapters/chapter2/hog_umap.py:175"}, "region": {"startLine": 1}}}]}, {"ruleId": "scanner-ae1441330c5c324e", "level": "note", "message": {"text": "Possibly dead Python function: step_plot"}, "properties": {"repobilityId": "571608d80ed3f33f", "scanner": "scanner-primary", "fingerprint": "ae1441330c5c324e", "layer": "software", "severity": "low", "confidence": 1.0, "tags": ["dead-code"]}, "locations": [{"physicalLocation": {"artifactLocation": {"uri": "chapters/chapter2/hog_umap.py:214"}, "region": {"startLine": 1}}}]}, {"ruleId": "scanner-354cd3fe2e96833e", "level": "note", "message": {"text": "Possibly dead Python function: compute_cluster_metrics_both_spaces"}, "properties": {"repobilityId": "608abc77a69460f1", "scanner": "scanner-primary", "fingerprint": "354cd3fe2e96833e", "layer": "software", "severity": "low", "confidence": 1.0, "tags": ["dead-code"]}, "locations": [{"physicalLocation": {"artifactLocation": {"uri": "chapters/chapter2/archive/scripts/sensitivity_analysis_corrected.py:90"}, "region": {"startLine": 1}}}]}, {"ruleId": "scanner-37005ec46406f1b9", "level": "note", "message": {"text": "Possibly dead Python function: compute_hog_centroids"}, "properties": {"repobilityId": "1a160340085b1081", "scanner": "scanner-primary", "fingerprint": "37005ec46406f1b9", "layer": "software", "severity": "low", "confidence": 1.0, "tags": ["dead-code"]}, "locations": [{"physicalLocation": {"artifactLocation": {"uri": "chapters/chapter2/archive/scripts/sensitivity_analysis.py:114"}, "region": {"startLine": 1}}}]}, {"ruleId": "scanner-ce6c55eaa12e0c1d", "level": "note", "message": {"text": "Possibly dead Python function: compute_silhouette_in_original_space"}, "properties": {"repobilityId": "cc3ecaf26de6a513", "scanner": "scanner-primary", "fingerprint": "ce6c55eaa12e0c1d", "layer": "software", "severity": "low", "confidence": 1.0, "tags": ["dead-code"]}, "locations": [{"physicalLocation": {"artifactLocation": {"uri": "chapters/chapter2/archive/scripts/deep_hog_analysis.py:71"}, "region": {"startLine": 1}}}]}, {"ruleId": "scanner-083ac8ccaeb73c75", "level": "note", "message": {"text": "Possibly dead Python function: normalize_label"}, "properties": {"repobilityId": "fd7e88e0164a7755", "scanner": "scanner-primary", "fingerprint": "083ac8ccaeb73c75", "layer": "software", "severity": "low", "confidence": 1.0, "tags": ["dead-code"]}, "locations": [{"physicalLocation": {"artifactLocation": {"uri": "projects/caffeine/lab/001_adora_expression/compare_labels_metadata.py:104"}, "region": {"startLine": 1}}}]}, {"ruleId": "scanner-f4dd0108b0026540", "level": "warning", "message": {"text": "Privileged port 10 in use"}, "properties": {"repobilityId": "735372d6b5594915", "scanner": "scanner-primary", "fingerprint": "f4dd0108b0026540", "layer": "network", "severity": "medium", "confidence": 1.0, "tags": ["security", "ports"]}, "locations": [{"physicalLocation": {"artifactLocation": {"uri": "chapters/chapter2/run_200epoch_sweep.sh"}, "region": {"startLine": 1}}}]}, {"ruleId": "scanner-62502203c2b4cc9f", "level": "warning", "message": {"text": "Privileged port 11 in use"}, "properties": {"repobilityId": "5b3038c67fabb4c8", "scanner": "scanner-primary", "fingerprint": "62502203c2b4cc9f", "layer": "network", "severity": "medium", "confidence": 1.0, "tags": ["security", "ports"]}, "locations": [{"physicalLocation": {"artifactLocation": {"uri": "chapters/chapter2/run_60epoch_scaled_lr.sh"}, "region": {"startLine": 1}}}]}, {"ruleId": "scanner-ae2b41fb3a1c87aa", "level": "warning", "message": {"text": "Privileged port 60 in use"}, "properties": {"repobilityId": "f4424efab727024f", "scanner": "scanner-primary", "fingerprint": "ae2b41fb3a1c87aa", "layer": "network", "severity": "medium", "confidence": 1.0, "tags": ["security", "ports"]}, "locations": [{"physicalLocation": {"artifactLocation": {"uri": "chapters/chapter2/run_60epoch_scaled_lr.sh"}, "region": {"startLine": 1}}}]}, {"ruleId": "scanner-a8088a874e539281", "level": "warning", "message": {"text": "Dockerfile runs as root: infra/github-runner/Dockerfile"}, "properties": {"repobilityId": "65d0a94ac76beef9", "scanner": "scanner-primary", "fingerprint": "a8088a874e539281", "layer": "hardware", "severity": "medium", "confidence": 1.0, "tags": ["security", "container"]}}, {"ruleId": "scanner-52e52cb8bd0219d6", "level": "note", "message": {"text": "Docker base image is tag-pinned but not digest-pinned: ubuntu:24.04"}, "properties": {"repobilityId": "191c3a452cc899df", "scanner": "scanner-primary", "fingerprint": "52e52cb8bd0219d6", "layer": "hardware", "severity": "low", "confidence": 1.0, "tags": ["supply-chain", "docker", "pinned-dependencies"]}, "locations": [{"physicalLocation": {"artifactLocation": {"uri": "infra/github-runner/Dockerfile"}, "region": {"startLine": 1}}}]}, {"ruleId": "scanner-18dc3fa21bb6af0b", "level": "warning", "message": {"text": "Insecure pattern 'direct_innerhtml_assignment' in chapters/chapter2/hog_umap_interactive.py:360"}, "properties": {"repobilityId": "5fbb6d6a243600fc", "scanner": "scanner-primary", "fingerprint": "18dc3fa21bb6af0b", "layer": "security", "severity": "medium", "confidence": 1.0, "tags": ["owasp", "direct_innerhtml_assignment"]}, "locations": [{"physicalLocation": {"artifactLocation": {"uri": "chapters/chapter2/hog_umap_interactive.py"}, "region": {"startLine": 360}}}]}, {"ruleId": "scanner-6372cebde0220094", "level": "warning", "message": {"text": "No auth library detected"}, "properties": {"repobilityId": "a5b6035a5bbf8054", "scanner": "scanner-primary", "fingerprint": "6372cebde0220094", "layer": "security", "severity": "medium", "confidence": 1.0, "tags": ["coverage", "auth"]}}, {"ruleId": "scanner-a2483bc396beed6d", "level": "note", "message": {"text": "GitHub Action is tag-pinned rather than SHA-pinned"}, "properties": {"repobilityId": "f2cac4f5723d8473", "scanner": "scanner-primary", "fingerprint": "a2483bc396beed6d", "layer": "cicd", "severity": "low", "confidence": 1.0, "tags": ["supply-chain", "github-actions", "pinned-dependencies"]}, "locations": [{"physicalLocation": {"artifactLocation": {"uri": ".github/workflows/hygiene.yml"}, "region": {"startLine": 17}}}]}, {"ruleId": "scanner-6893a6c8b0861585", "level": "warning", "message": {"text": "Very low test-to-source ratio"}, "properties": {"repobilityId": "54a7de3f06314bf0", "scanner": "scanner-primary", "fingerprint": "6893a6c8b0861585", "layer": "quality", "severity": "medium", "confidence": 1.0, "tags": ["tests", "coverage"]}}, {"ruleId": "scanner-141b30a41e03817b", "level": "note", "message": {"text": "No license file detected"}, "properties": {"repobilityId": "87bf7164a25a9ee6", "scanner": "scanner-primary", "fingerprint": "141b30a41e03817b", "layer": "quality", "severity": "low", "confidence": 1.0, "tags": ["license", "repo-hardening", "generated-repo-pattern"]}}, {"ruleId": "scanner-3ab5d313dda8e5f9", "level": "note", "message": {"text": "Debug logging residue appears in source files"}, "properties": {"repobilityId": "2f57d74e43184a9c", "scanner": "scanner-primary", "fingerprint": "3ab5d313dda8e5f9", "layer": "quality", "severity": "low", "confidence": 1.0, "tags": ["debug", "cleanup", "repo-hardening", "generated-repo-pattern"]}}, {"ruleId": "scanner-11825279136b53a3", "level": "warning", "message": {"text": "CI is configured but no tests are detected"}, "properties": {"repobilityId": "cebdfc063fc19ec9", "scanner": "scanner-primary", "fingerprint": "11825279136b53a3", "layer": "quality", "severity": "medium", "confidence": 1.0, "tags": ["tests", "ci", "config-theater", "repo-hardening", "generated-repo-pattern"]}}, {"ruleId": "scanner-b9088664ace7f748", "level": "note", "message": {"text": "Composite production-readiness gap"}, "properties": {"repobilityId": "1f92452505d7b22f", "scanner": "scanner-primary", 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