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aristoteleo/PantheonOS

https://github.com/aristoteleo/PantheonOS · scanned 2026-06-17 01:36 UTC (1 month, 2 weeks ago)

169 raw signals (0 security + 169 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 -28.9 (diff) · 131 actionable findings from 1 signal source. 38 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
47.8
/100
Security checks
48
0 findings
System graph
48
77.8% cov · 131 findings
Critical
1
click to filter
Agents
10
0 votes
Crowd
0
reported
Severity distribution — click a segment to filter
Active filters: excluding tests × Reset all
Severity: Critical 1 High 12 Medium 16 Low 65 9-Layer: Software Security Quality Integrity Frontend Hardware Data Network Cicd Source: Security checks 0 System graph 131 Crowd 0 Layer: Software 17 Network 1 Hardware 2 Security 12 Cicd 4 Quality 95
Scan summary Repository scanned at 47.8/100 with 77.8% coverage. It contains 8304 nodes across 0 cross-layer flows, written primarily in mixed languages. Engine surfaced 169 findings — concentrated in quality (112), software (25), cicd (16). Risk profile is high: 1 critical, 12 high, 24 medium. Recommended next step: open the quality layer findings first — that's where the highest-impact wins live.

Showing 93 of 131 actionable findings. 169 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.

high System graph quality Integrity conf 1.00 Blocking `time.sleep(...)` inside `async def _process_message` — pantheon/repl/core.py:1396
Sync I/O inside an async function blocks the event loop. While `time.sleep(...)` is running, *all* other coroutines on this loop are paused — silent throughput collapse under concurrency. Use the async equivalent (`httpx.AsyncClient`, `asyncio.sleep`, `aiofiles`) or wrap with `await asyncio.to_thre…
pantheon/repl/core.py:1396 Sync io in asyncPerformance
high System graph quality Integrity conf 1.00 Blocking `urllib.request.urlopen(...)` inside `async def web_fetch` — pantheon/toolsets/web_urllib.py:324
Sync I/O inside an async function blocks the event loop. While `urllib.request.urlopen(...)` is running, *all* other coroutines on this loop are paused — silent throughput collapse under concurrency. Use the async equivalent (`httpx.AsyncClient`, `asyncio.sleep`, `aiofiles`) or wrap with `await asy…
pantheon/toolsets/web_urllib.py:324 Sync io in asyncPerformance
high System graph cicd CI/CD security conf 1.00 GitHub Action tracks a moving branch
aquasecurity/trivy-action@master can move without a code change in this repo. Pin third-party actions to a reviewed 40-character commit SHA.
.github/workflows/docker-build.yml:163 CI/CD securitySupply chainGithub actions
high System graph security security conf 1.00 Insecure pattern 'eval_used' in cmd2func/config.py:43
Found a known-risky pattern (eval_used). Review and replace if possible.
cmd2func/config.py:43 Eval used
high System graph security security conf 1.00 Insecure pattern 'eval_used' in funcdesc/parse.py:114
Found a known-risky pattern (eval_used). Review and replace if possible.
funcdesc/parse.py:114 Eval used
high System graph security security conf 1.00 Insecure pattern 'eval_used' in funcdesc/utils/json.py:77
Found a known-risky pattern (eval_used). Review and replace if possible.
funcdesc/utils/json.py:77 Eval used
high System graph security security conf 1.00 Insecure pattern 'eval_used' in pantheon/toolsets/python/python_interpreter.py:30
Found a known-risky pattern (eval_used). Review and replace if possible.
pantheon/toolsets/python/python_interpreter.py:30 Eval used
high System graph security security conf 1.00 Insecure pattern 'exec_used' in pantheon/toolsets/python/python_interpreter.py:34
Found a known-risky pattern (exec_used). Review and replace if possible.
pantheon/toolsets/python/python_interpreter.py:34 Exec used
high System graph security security conf 1.00 Insecure pattern 'python_os_system' in pantheon/__main__.py:33
Found a known-risky pattern (python_os_system). Review and replace if possible.
pantheon/__main__.py:33 Python os system
high System graph security security conf 1.00 Insecure pattern 'python_os_system' in pantheon/repl/__main__.py:37
Found a known-risky pattern (python_os_system). Review and replace if possible.
pantheon/repl/__main__.py:37 Python os system
high System graph security security conf 1.00 Insecure pattern 'subprocess_shell_true' in pantheon/repl/handlers/builtin/bash.py:24
Found a known-risky pattern (subprocess_shell_true). Review and replace if possible.
pantheon/repl/handlers/builtin/bash.py:24 Subprocess shell true
high System graph security security conf 1.00 Insecure pattern 'tls_verify_false' in pantheon/toolsets/web_urllib.py:266
Found a known-risky pattern (tls_verify_false). Review and replace if possible.
pantheon/toolsets/web_urllib.py:266 Tls verify false
medium System graph quality Integrity conf 1.00 `fetch()` without try/.catch or AbortSignal — pantheon/factory/templates/skills/live_view/spatial3d/adapter.js:43
Bare `fetch(...)` will throw an unhandled rejection on network failure. Wrap in try/catch, attach a `.catch(...)`, or pass an AbortSignal with a timeout.
runtime safetyRobustness
medium System graph quality Agent instructions conf 1.00 Agent authority lacks a verifier contract: pantheon/factory/templates/mcp.json
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.
pantheon/factory/templates/mcp.json VerificationMcp config
medium System graph quality Agent instructions conf 1.00 Agent authority lacks a verifier contract: pantheon/factory/templates/skills/omics/database_access/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.
pantheon/factory/templates/skills/omics/database_access/SKILL.md VerificationSkill file
medium System graph quality Agent instructions conf 1.00 Agent authority lacks a verifier contract: pantheon/factory/templates/skills/omics/gene_panel_selection/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.
pantheon/factory/templates/skills/omics/gene_panel_selection/SKILL.md VerificationSkill file
medium System graph quality Agent instructions conf 1.00 Agent authority lacks a verifier contract: pantheon/factory/templates/skills/omics/scfm/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.
pantheon/factory/templates/skills/omics/scfm/SKILL.md VerificationSkill file
medium System graph quality Agent instructions conf 1.00 Agent authority lacks a verifier contract: pantheon/factory/templates/skills/omics/upstream_processing/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.
pantheon/factory/templates/skills/omics/upstream_processing/SKILL.md VerificationSkill file
medium System graph quality Agent instructions conf 1.00 Agent authority lacks a verifier contract: pantheon/factory/templates/skills/structural_biology/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.
pantheon/factory/templates/skills/structural_biology/SKILL.md VerificationSkill file
medium System graph security Agent instructions conf 1.00 Agent instruction contains unpinned remote install: pantheon/factory/templates/mcp.json
Remote install commands in agent instructions are a supply-chain risk, especially when an agent can execute shell commands.
pantheon/factory/templates/mcp.json:43 Supply chainMcp config
medium System graph quality Placeholder conf 1.00 Critical user flow still appears backed by mock or placeholder data
A payment/auth/admin/order/billing-style flow contains mock, fake, TODO, dummy, or placeholder markers in runtime source. In the Fable corpus this is a high-leverage completeness smell: the app can look finished while the money, identity, or tenant flow is still scaffolded.
Mock dataCritical flowGenerated repo pattern
medium System graph hardware Security conf 1.00 Dockerfile runs as root: docker/Dockerfile
No non-root USER set. Containers running as root expand the blast radius of any vulnerability inside the image.
Container
medium System graph cicd CI/CD security conf 1.00 9 occurrences GitHub Action is tag-pinned rather than SHA-pinned
docker/setup-qemu-action@v3 can move without a code change in this repo. Pin third-party actions to a reviewed 40-character commit SHA.
3 files, 9 locations
.github/workflows/docker-build.yml:53, 58, 66, 73, 99, 173, 183 (7 hits)
.github/workflows/promote-agent.yml:39
.github/workflows/test.yml:49
CI/CD securitySupply chainGithub actions
medium System graph cicd CI/CD security conf 1.00 GitHub Actions workflow grants broad write permissions
CI tokens with write permissions increase blast radius when an action, dependency, or PR workflow is compromised. Prefer job-level least-privilege permissions.
.github/workflows/docker-build.yml CI/CD securitySupply chainGithub actions
medium System graph security security conf 1.00 Insecure pattern 'direct_innerhtml_assignment' in pantheon/evolution/visualizer.py:1941
Found a known-risky pattern (direct_innerhtml_assignment). Review and replace if possible.
pantheon/evolution/visualizer.py:1941 Direct innerhtml assignment
medium System graph quality Integrity conf 1.00 Network/subprocess call without timeout or try/except — pantheon/store/seed.py:334
`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 Placeholder conf 1.00 Placeholder or mock-heavy implementation detected
Found 105 placeholder/mock markers across 36 source files. This often means the repo looks complete while core flows still use generated scaffolding or fake data.
Mock dataIncompleteGenerated repo pattern
medium System graph network Security conf 1.00 Privileged port 127 in use
Port 127 is privileged (<1024). Make sure the service runs with the right caps or front it with a non-privileged port via a load balancer.
pantheon/toolsets/live_view/data_server.py Ports
low System graph quality Debug conf 1.00 Debug logging residue appears in source files
Found 702 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 2 occurrences Docker base image is tag-pinned but not digest-pinned: python:3.12-slim-bookworm
Container tags can be retagged upstream. Pin production base images to a reviewed digest (`image@sha256:...`) when reproducibility and supply-chain integrity matter.
lines 4, 163
docker/Dockerfile:4, 163 (2 hits)
containersPinned dependencies
low System graph cicd CI/CD security conf 1.00 5 occurrences 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.
3 files, 5 locations
.github/workflows/test.yml:30, 35, 82 (3 hits)
.github/workflows/docker-build.yml:43
.github/workflows/publish_pypi.yml:19
CI/CD securitySupply chainGithub actions
low System graph quality Integrity conf 1.00 9 occurrences Near-duplicate function bodies in 2 places
Functions with the same first-5-line body hash: scripts/benchmark_multi_provider.py:est_tokens, scripts/benchmark_token_optimizations.py:est_tokens This is *the* AI-coder failure mode (4× more duplication in vibe-coded repos — see https://jw.hn/ai-code-hygiene). Consolidate or document why they're…
9 occurrences
repo-level (9 hits)
duplicatesduplication
low System graph quality Integrity conf 1.00 5 occurrences Near-duplicate function bodies in 4 places
Functions with the same first-5-line body hash: examples/evolution_batch_correction/evolution_harmonypy/harmony.py:Z_corr, examples/evolution_batch_correction/evolution_harmonypy/results/harmony_optimized.py:Z_corr, examples/evolution_batch_correction/evolution_harmonypy/results/harmony_272.py:Z_co…
5 occurrences
repo-level (5 hits)
duplicatesduplication
low System graph quality Integrity conf 1.00 6 occurrences Near-duplicate function bodies in 5 places
Functions with the same first-5-line body hash: examples/evolution_batch_correction/evolution_harmonypy/run_evolution.py:run_evolution, examples/evolution_batch_correction/evolution_scanorama/run_evolution.py:run_evolution, examples/evolution_batch_correction/evolution_bbknn/run_evolution.py:run_ev…
6 occurrences
repo-level (6 hits)
duplicatesduplication
low System graph quality Integrity conf 1.00 Old/deprecated-named symbol `_evict_old` in pantheon/background.py:142
Names with suffixes like `_old`, `_v1`, `_deprecated` usually indicate replaced-but-not-removed code (typical AI-coder leftover). Confirm and delete, or rename if it's the active version.
old markerDead code
low System graph quality Integrity conf 1.00 Old/deprecated-named symbol `adata_copy` in examples/evolution_gene_panel/scripts/run_preprocessing.py:42
Names with suffixes like `_old`, `_v1`, `_deprecated` usually indicate replaced-but-not-removed code (typical AI-coder leftover). Confirm and delete, or rename if it's the active version.
old markerDead code
low System graph quality Integrity conf 1.00 Old/deprecated-named symbol `all_timestamps_old` in scripts/benchmark_token_optimizations.py:90
Names with suffixes like `_old`, `_v1`, `_deprecated` usually indicate replaced-but-not-removed code (typical AI-coder leftover). Confirm and delete, or rename if it's the active version.
old markerDead code
low System graph quality Integrity conf 1.00 Old/deprecated-named symbol `clear_old` in executor/engine/manager.py:55
Names with suffixes like `_old`, `_v1`, `_deprecated` usually indicate replaced-but-not-removed code (typical AI-coder leftover). Confirm and delete, or rename if it's the active version.
old markerDead code
low System graph quality Integrity conf 1.00 Old/deprecated-named symbol `files_upload_v2` in pantheon/claw/channels/slack.py:180
Names with suffixes like `_old`, `_v1`, `_deprecated` usually indicate replaced-but-not-removed code (typical AI-coder leftover). Confirm and delete, or rename if it's the active version.
old markerDead code
low System graph quality Integrity conf 1.00 Old/deprecated-named symbol `logp_old` in examples/evolution_gene_panel/results_explore_primary/rl_gene_panel_optimized.py:256
Names with suffixes like `_old`, `_v1`, `_deprecated` usually indicate replaced-but-not-removed code (typical AI-coder leftover). Confirm and delete, or rename if it's the active version.
old markerDead code
low System graph quality Integrity conf 1.00 Old/deprecated-named symbol `logp_old` in examples/evolution_gene_panel/results_optimize_primary/rl_gene_panel_optimized.py:248
Names with suffixes like `_old`, `_v1`, `_deprecated` usually indicate replaced-but-not-removed code (typical AI-coder leftover). Confirm and delete, or rename if it's the active version.
old markerDead code
low System graph quality Integrity conf 1.00 Old/deprecated-named symbol `msg_copy` in pantheon/internal/memory/memory.py:384
Names with suffixes like `_old`, `_v1`, `_deprecated` usually indicate replaced-but-not-removed code (typical AI-coder leftover). Confirm and delete, or rename if it's the active version.
old markerDead code
low System graph quality Integrity conf 1.00 Old/deprecated-named symbol `needs_copy` in pantheon/toolsets/scfm/adapters/uce.py:388
Names with suffixes like `_old`, `_v1`, `_deprecated` usually indicate replaced-but-not-removed code (typical AI-coder leftover). Confirm and delete, or rename if it's the active version.
old markerDead code
low System graph quality Integrity conf 1.00 Old/deprecated-named symbol `nOld` in tests/test_learning_system/test_extractor.py:81
Names with suffixes like `_old`, `_v1`, `_deprecated` usually indicate replaced-but-not-removed code (typical AI-coder leftover). Confirm and delete, or rename if it's the active version.
old markerDead code
low System graph quality Integrity conf 1.00 Old/deprecated-named symbol `obj_old` in examples/evolution_batch_correction/evolution_harmonypy/harmony.py:526
Names with suffixes like `_old`, `_v1`, `_deprecated` usually indicate replaced-but-not-removed code (typical AI-coder leftover). Confirm and delete, or rename if it's the active version.
old markerDead code
low System graph quality Integrity conf 1.00 Old/deprecated-named symbol `obj_old` in examples/evolution_batch_correction/evolution_harmonypy/results/harmony.py:646
Names with suffixes like `_old`, `_v1`, `_deprecated` usually indicate replaced-but-not-removed code (typical AI-coder leftover). Confirm and delete, or rename if it's the active version.
old markerDead code
low System graph quality Integrity conf 1.00 Old/deprecated-named symbol `obj_old` in examples/evolution_batch_correction/evolution_harmonypy/results/harmony_272.py:631
Names with suffixes like `_old`, `_v1`, `_deprecated` usually indicate replaced-but-not-removed code (typical AI-coder leftover). Confirm and delete, or rename if it's the active version.
old markerDead code
low System graph quality Integrity conf 1.00 Old/deprecated-named symbol `obj_old` in examples/evolution_batch_correction/evolution_harmonypy/results/harmony_best_mixing.py:697
Names with suffixes like `_old`, `_v1`, `_deprecated` usually indicate replaced-but-not-removed code (typical AI-coder leftover). Confirm and delete, or rename if it's the active version.
old markerDead code
low System graph quality Integrity conf 1.00 Old/deprecated-named symbol `obj_old` in examples/evolution_batch_correction/evolution_harmonypy/results/harmony_optimized.py:646
Names with suffixes like `_old`, `_v1`, `_deprecated` usually indicate replaced-but-not-removed code (typical AI-coder leftover). Confirm and delete, or rename if it's the active version.
old markerDead code
low System graph quality Integrity conf 1.00 Old/deprecated-named symbol `receive_v1` in pantheon/claw/channels/feishu.py:23
Names with suffixes like `_old`, `_v1`, `_deprecated` usually indicate replaced-but-not-removed code (typical AI-coder leftover). Confirm and delete, or rename if it's the active version.
old markerDead code
low System graph quality Integrity conf 1.00 Old/deprecated-named symbol `test_glm_5_deprecated` in tests/test_glm_5_1_support.py:35
Names with suffixes like `_old`, `_v1`, `_deprecated` usually indicate replaced-but-not-removed code (typical AI-coder leftover). Confirm and delete, or rename if it's the active version.
old markerDead code
low System graph quality Integrity conf 1.00 Old/deprecated-named symbol `X_old` in examples/evolution_batch_correction/evolution_scanorama/results/scanorama_optimized/scanorama.py:352
Names with suffixes like `_old`, `_v1`, `_deprecated` usually indicate replaced-but-not-removed code (typical AI-coder leftover). Confirm and delete, or rename if it's the active version.
old markerDead code
low System graph quality Integrity conf 1.00 Old/deprecated-named symbol `X_old` in examples/evolution_batch_correction/evolution_scanorama/scanorama/scanorama.py:349
Names with suffixes like `_old`, `_v1`, `_deprecated` usually indicate replaced-but-not-removed code (typical AI-coder leftover). Confirm and delete, or rename if it's the active version.
old markerDead code
low System graph software Dead code conf 1.00 Possibly dead Python function: assemble_accum
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
examples/evolution_batch_correction/evolution_scanorama/scanorama/scanorama.py:1010
low System graph software Dead code conf 1.00 Possibly dead Python function: assemble_accum
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
examples/evolution_batch_correction/evolution_scanorama/results/scanorama_optimized/scanorama.py:1393
low System graph software Dead code conf 1.00 Possibly dead Python function: beta_tool
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
scripts/benchmark_prompt_cache.py:44
low System graph software Dead code conf 1.00 Possibly dead Python function: chars_to_tokens
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
scripts/benchmark_token_optimization_live.py:45
low System graph software Dead code conf 1.00 Possibly dead Python function: correct_scanpy
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
examples/evolution_batch_correction/evolution_scanorama/scanorama/scanorama.py:195
low System graph software Dead code conf 1.00 Possibly dead Python function: correct_scanpy
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
examples/evolution_batch_correction/evolution_scanorama/results/scanorama_optimized/scanorama.py:198
low System graph software Dead code conf 1.00 5 occurrences Possibly dead Python function: extract_cell_connectivity
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
5 files, 5 locations
examples/evolution_batch_correction/evolution_bbknn/bbknn/__init__.py:210
examples/evolution_batch_correction/evolution_bbknn/results/bbknn_balanced/__init__.py:210
examples/evolution_batch_correction/evolution_bbknn/results/bbknn_fast/__init__.py:210
examples/evolution_batch_correction/evolution_bbknn/results/bbknn_optimized/__init__.py:210
examples/evolution_batch_correction/evolution_bbknn/results/bbknn_similar_speed/__init__.py:210
low System graph software Dead code conf 1.00 Possibly dead Python function: generate_test_data
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
examples/evolution_batch_correction/evolution_harmonypy/evaluator.py:100
low System graph software Dead code conf 1.00 Possibly dead Python function: integrate_scanpy
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
examples/evolution_batch_correction/evolution_scanorama/scanorama/scanorama.py:262
low System graph software Dead code conf 1.00 Possibly dead Python function: integrate_scanpy
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
examples/evolution_batch_correction/evolution_scanorama/results/scanorama_optimized/scanorama.py:265
low System graph software Dead code conf 1.00 Possibly dead Python function: mkdir_p
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
examples/evolution_batch_correction/evolution_scanorama/scanorama/utils.py:112
low System graph software Dead code conf 1.00 Possibly dead Python function: mkdir_p
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
examples/evolution_batch_correction/evolution_scanorama/results/scanorama_optimized/utils.py:112
low System graph software Dead code conf 1.00 Possibly dead Python function: profiled_start_toolset_unified
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
scripts/profile_builtin_startup.py:178
low System graph software Dead code conf 1.00 Possibly dead Python function: pseudobulk
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
examples/evolution_topact/topact/spatial.py:380
low System graph software Dead code conf 1.00 5 occurrences Possibly dead Python function: ridge_regression
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
5 files, 5 locations
examples/evolution_batch_correction/evolution_bbknn/bbknn/__init__.py:133
examples/evolution_batch_correction/evolution_bbknn/results/bbknn_balanced/__init__.py:133
examples/evolution_batch_correction/evolution_bbknn/results/bbknn_fast/__init__.py:133
examples/evolution_batch_correction/evolution_bbknn/results/bbknn_optimized/__init__.py:133
examples/evolution_batch_correction/evolution_bbknn/results/bbknn_similar_speed/__init__.py:133
low System graph software Dead code conf 1.00 Possibly dead Python function: visualize_dropout
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
examples/evolution_batch_correction/evolution_scanorama/scanorama/utils.py:84
low System graph software Dead code conf 1.00 Possibly dead Python function: visualize_dropout
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
examples/evolution_batch_correction/evolution_scanorama/results/scanorama_optimized/utils.py:84
low System graph quality Integrity conf 1.00 Stub function `async_setup` (body is just `pass`/`return`) — pantheon/team/base.py:14
Likely an AI scaffold that was never filled in. Remove or implement.
Empty handlerDead code
low System graph quality Integrity conf 1.00 Stub function `cleanup` (body is just `pass`/`return`) — pantheon/toolset.py:361
Likely an AI scaffold that was never filled in. Remove or implement.
Empty handlerDead code
low System graph quality Integrity conf 1.00 Stub function `close` (body is just `pass`/`return`) — pantheon/remote/backend/nats.py:420
Likely an AI scaffold that was never filled in. Remove or implement.
Empty handlerDead code
low System graph quality Integrity conf 1.00 Stub function `insert` (body is just `pass`/`return`) — pantheon/toolsets/rag/wrap.py:5
Likely an AI scaffold that was never filled in. Remove or implement.
Empty handlerDead code
low System graph quality Integrity conf 1.00 Stub function `log_message` (body is just `pass`/`return`) — pantheon/utils/oauth/gemini.py:716
Likely an AI scaffold that was never filled in. Remove or implement.
Empty handlerDead code
low System graph quality Integrity conf 1.00 Stub function `on_run_start` (body is just `pass`/`return`) — pantheon/internal/learning_system/plugin.py:48
Likely an AI scaffold that was never filled in. Remove or implement.
Empty handlerDead code
low System graph quality Integrity conf 1.00 Stub function `save_metadata` (body is just `pass`/`return`) — pantheon/internal/memory/storage.py:55
Likely an AI scaffold that was never filled in. Remove or implement.
Empty handlerDead code
low System graph quality Integrity conf 1.00 Stub function `servers` (body is just `pass`/`return`) — pantheon/remote/backend/base.py:76
Likely an AI scaffold that was never filled in. Remove or implement.
Empty handlerDead code
low System graph quality Complexity conf 1.00 Very large file: examples/evolution_batch_correction/evolution_scanorama/results/scanorama_optimized/scanorama.py (1415 lines)
Files with >800 lines often hide complexity hotspots and discourage tests.
low System graph quality Complexity conf 1.00 Very large file: examples/evolution_gene_panel/results_explore_primary/rl_gene_panel_optimized.py (1377 lines)
Files with >800 lines often hide complexity hotspots and discourage tests.
low System graph quality Complexity conf 1.00 Very large file: pantheon/agent.py (2937 lines)
Files with >800 lines often hide complexity hotspots and discourage tests.
low System graph quality Complexity conf 1.00 Very large file: pantheon/chatroom/room.py (3934 lines)
Files with >800 lines often hide complexity hotspots and discourage tests.
low System graph quality Complexity conf 1.00 Very large file: pantheon/evolution/team.py (1335 lines)
Files with >800 lines often hide complexity hotspots and discourage tests.
low System graph quality Complexity conf 1.00 Very large file: pantheon/evolution/visualizer.py (4344 lines)
Files with >800 lines often hide complexity hotspots and discourage tests.
low System graph quality Complexity conf 1.00 Very large file: pantheon/repl/core.py (2525 lines)
Files with >800 lines often hide complexity hotspots and discourage tests.
low System graph quality Complexity conf 1.00 Very large file: pantheon/repl/prompt_app.py (1549 lines)
Files with >800 lines often hide complexity hotspots and discourage tests.
low System graph quality Complexity conf 1.00 Very large file: pantheon/toolsets/evolution/evolution_toolset.py (1633 lines)
Files with >800 lines often hide complexity hotspots and discourage tests.
low System graph quality Complexity conf 1.00 Very large file: pantheon/toolsets/file/file_manager.py (2124 lines)
Files with >800 lines often hide complexity hotspots and discourage tests.
low System graph quality Complexity conf 1.00 Very large file: pantheon/toolsets/notebook/integrated_notebook.py (2092 lines)
Files with >800 lines often hide complexity hotspots and discourage tests.
low System graph quality Complexity conf 1.00 Very large file: pantheon/utils/llm.py (1887 lines)
Files with >800 lines often hide complexity hotspots and discourage tests.
low System graph quality Complexity conf 1.00 Very large file: pantheon/utils/token_optimization.py (2421 lines)
Files with >800 lines often hide complexity hotspots and discourage tests.
low System graph quality Complexity conf 1.00 Very large file: tests/test_scfm.py (2131 lines)
Files with >800 lines often hide complexity hotspots and discourage tests.
low System graph quality Complexity conf 1.00 Very large file: tests/test_token_optimization.py (1725 lines)
Files with >800 lines often hide complexity hotspots and discourage tests.
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