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acefesan/dl-bio

https://github.com/acefesan/dl-bio · scanned 2026-06-17 01:28 UTC (1 month, 2 weeks ago)

47 raw signals (0 security + 47 graph)

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UNIFIED Repobility · multi-layer engine · AI coders

Complete repo analysis

Last scanned 1 month, 2 weeks ago · v2 · last Δ -15.8 (diff) · 28 actionable findings from 1 signal source. 19 repeated signals grouped for readability. Security checks, system graph analysis, and verified AI-agent feedback are merged into one review queue.

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Combined
60.9
/100
Security checks
61
0 findings
System graph
61
66.7% cov · 28 findings
Critical
0
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Agents
10
0 votes
Crowd
0
reported
Severity distribution — click a segment to filter
Active filters: excluding tests × Reset all
Severity: Critical 0 High 0 Medium 13 Low 15 9-Layer: Software Security Quality Integrity Frontend Hardware Data Network Cicd Source: Security checks 0 System graph 28 Crowd 0 Layer: Software 9 Network 3 Hardware 2 Security 2 Cicd 1 Quality 11
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Scan summary Repository scanned at 60.9/100 with 66.7% coverage. It contains 752 nodes across 0 cross-layer flows, written primarily in mixed languages. Engine surfaced 47 findings — concentrated in quality (30), software (9), network (3). Risk profile is low: 0 critical, 0 high, 13 medium. Recommended next step: open the quality layer findings first — that's where the highest-impact wins live.

Showing 28 of 28 actionable findings. 47 raw detector signals were grouped into reader-sized issues. Click TP / FP to vote on a finding's accuracy — votes adjust the confidence weighting and improve detection across the platform.

medium System graph quality Agent instructions conf 1.00 Agent authority lacks a verifier contract: .claude/skills/orchestrate/SKILL.md
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.
.claude/skills/orchestrate/SKILL.md VerificationClaude instruction
medium System graph quality Agent instructions conf 1.00 Agent authority lacks a verifier contract: AGENTS.md
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.
AGENTS.md VerificationAgents md
medium System graph quality Agent instructions conf 1.00 Agent instructions exist but release-hardening basics are missing
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.
Repo hardeningGenerated repo pattern
medium System graph quality Tests conf 1.00 CI is configured but no tests are detected
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.
CI/CDConfig theaterRepo hardening
medium System graph hardware Security conf 1.00 Dockerfile runs as root: infra/github-runner/Dockerfile
No non-root USER set. Containers running as root expand the blast radius of any vulnerability inside the image.
Container
medium System graph security security conf 1.00 Insecure pattern 'direct_innerhtml_assignment' in chapters/chapter2/hog_umap_interactive.py:360
Found a known-risky pattern (direct_innerhtml_assignment). Review and replace if possible.
chapters/chapter2/hog_umap_interactive.py:360 Direct innerhtml assignment
medium System graph quality Integrity conf 1.00 Network/subprocess call without timeout or try/except — chapters/chapter2/run.py:117
`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.
runtime safetyRobustness
medium System graph quality Integrity conf 1.00 Network/subprocess call without timeout or try/except — write_artifact_metadata.py:31
`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.
runtime safetyRobustness
medium System graph security Coverage conf 1.00 No auth library detected
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.
auth
medium System graph network Security conf 1.00 Privileged port 10 in use
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.
chapters/chapter2/run_200epoch_sweep.sh Ports
medium System graph network Security conf 1.00 Privileged port 11 in use
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.
chapters/chapter2/run_60epoch_scaled_lr.sh Ports
medium System graph network Security conf 1.00 Privileged port 60 in use
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.
chapters/chapter2/run_60epoch_scaled_lr.sh Ports
medium System graph quality Tests conf 1.00 Very low test-to-source ratio
0 test file(s) for 41 source file(s) (ratio 0.00). Consider adding integration or unit tests for critical paths.
Coverage
low System graph quality Production readiness conf 1.00 Composite production-readiness gap
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.
Repo hardeningGenerated repo pattern
low System graph quality Debug conf 1.00 Debug logging residue appears in source files
Found 772 console/debugger/print-style debug statements in non-test source. This is a common fast-generation residue before production cleanup.
CleanupRepo hardeningGenerated repo pattern
low System graph hardware Supply chain conf 1.00 Docker base image is tag-pinned but not digest-pinned: ubuntu:24.04
Container tags can be retagged upstream. Pin production base images to a reviewed digest (`image@sha256:...`) when reproducibility and supply-chain integrity matter.
infra/github-runner/Dockerfile:1 containersPinned dependencies
low System graph cicd CI/CD security conf 1.00 GitHub Action is tag-pinned rather than SHA-pinned
actions/checkout@v4 can move without a code change in this repo. Pin third-party actions to a reviewed 40-character commit SHA.
.github/workflows/hygiene.yml:17 CI/CD securitySupply chainGithub actions
low System graph quality Integrity conf 1.00 20 occurrences Near-duplicate function bodies in 2 places
Functions with the same first-5-line body hash: chapters/chapter2/02_build_dataset.py:load_sequences, chapters/chapter2/archive/scripts/build_cafa3_dataset.py:load_sequences This is *the* AI-coder failure mode (4× more duplication in vibe-coded repos — see https://jw.hn/ai-code-hygiene). Consolida…
20 occurrences
repo-level (20 hits)
duplicatesduplication
low System graph quality License conf 1.00 No license file detected
No LICENSE/COPYING/NOTICE file was found. Generated repositories often omit licensing, which blocks reuse and automated intake.
Repo hardeningGenerated repo pattern
low System graph software Dead code conf 1.00 Possibly dead Python function: compute_cluster_metrics_both_spaces
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
chapters/chapter2/archive/scripts/sensitivity_analysis_corrected.py:90
low System graph software Dead code conf 1.00 Possibly dead Python function: compute_hog_centroids
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
chapters/chapter2/archive/scripts/sensitivity_analysis.py:114
low System graph software Dead code conf 1.00 Possibly dead Python function: compute_silhouette_in_original_space
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
chapters/chapter2/archive/scripts/deep_hog_analysis.py:71
low System graph software Dead code conf 1.00 Possibly dead Python function: loss_fn
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
chapters/chapter2/05_go_prediction.py:119
low System graph software Dead code conf 1.00 Possibly dead Python function: loss_fn
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
chapters/chapter2/06_go_grid_search.py:111
low System graph software Dead code conf 1.00 Possibly dead Python function: normalize_label
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
projects/caffeine/lab/001_adora_expression/compare_labels_metadata.py:104
low System graph software Dead code conf 1.00 Possibly dead Python function: step_embed
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
chapters/chapter2/hog_umap.py:175
low System graph software Dead code conf 1.00 Possibly dead Python function: step_extract
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
chapters/chapter2/hog_umap.py:76
low System graph software Dead code conf 1.00 Possibly dead Python function: step_plot
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
chapters/chapter2/hog_umap.py:214
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