The open-source AI workbench for scientific research
This report presents the forensic synthetic code analysis of synthetic-sciences/openscience, a TypeScript project with 3,355 GitHub stars. SynthScan v2.0 examined 1,054,008 lines of code across 3405 source files, recording 3849 pattern matches distributed across 25 syntactic categories. The overall adjusted score of 6.9 places this repository in the Low AI signal band.
The scanner applied 160+ deterministic lexical heuristics, multi-line block detectors, abstract syntax tree depth profilers, and a cross-file Jaccard similarity matrix to construct a statistically normalised synthetic code estimate. All matches are individually weighted by severity coefficient and contextual multiplier before summation, and the resulting headline score is temporally discounted to account for the repository's development history relative to the commercial emergence of large language model coding tooling (November 2022 onward).
Longitudinal tracking requires multiple scan runs. Once this repository is re-scanned after new commits land, this chart will visualise how the synthetic code signal evolves over time — enabling you to detect whether AI authorship is growing, stabilising, or being actively corrected by human engineers.
Classifies detected patterns by their diagnostic confidence and structural impact. CRITICAL patterns (coefficient 10) represent definitive synthetic signatures — hallucinated imports, explicit LLM attribution metadata — virtually never produced by human authors. HIGH (5) indicates strong structural tells such as cross-file repetition or cross-linguistic idioms. MEDIUM (2) covers recognisable conversational padding and AI-specific vocabulary. LOW (1) captures subtle indicators like tautological comments and generic boilerplate that require density to carry independent signal.
This horizontal bar chart decomposes the repository's raw synthetic code score by top-level directory, allowing you to pinpoint precisely which modules or components carry the highest AI authorship density. Directories with disproportionately high scores relative to their size warrant targeted manual review: concentrated AI signatures often trace back to mass-generated configuration layers, auto-ported test suites, LLM-scaffolded boilerplate classes, or entire subsystems authored under heavy copilot assistance. Use this view to prioritise your human code-review effort.
The scanner identified 3849 distinct pattern matches across 25 syntactic categories. Each entry below represents a discrete location in the source code where the engine recorded a statistically significant AI authorship indicator. Expand any category row to inspect the individual file paths, line numbers, code snippets, and the lexical context (CODE, COMMENT, or STRING) in which each match was detected.
Reading the findings table: The Severity column indicates the diagnostic confidence level (CRITICAL / HIGH / MEDIUM / LOW). The Context column identifies whether the match occurred inside executable code, an inline comment, or a string literal — comment-context matches receive a ×1.5 weight because LLMs systematically over-annotate. The ⚡ bolt icon marks clustered matches: three or more patterns within a 10-line window, each receiving an additional ×1.5 density multiplier as dense clusters constitute far stronger evidence of synthetic authorship than isolated hits.
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| MEDIUM | frontend/workspace/src/artifacts/inspector.ts | 134 | // ── Historical review records (provenance graph) ──────────────────────────── | COMMENT |
| MEDIUM | frontend/workspace/src/science/renderers/index.ts | 19 | // ── renderer registrations ───────────────────────────────────────────────── | COMMENT |
| MEDIUM | frontend/workspace/src/science/renderers/index.ts | 29 | // ──────────────────────────────────────────────────────────────────────────── | COMMENT |
| MEDIUM | frontend/workspace/src/components/settings/_shared.tsx | 146 | // ── Toolbar pieces ────────────────────────────────────────────────────────── | COMMENT |
| MEDIUM | frontend/workspace/src/components/settings/registry.ts | 4 | // ── Panel contract ────────────────────────────────────────────────────────── | COMMENT |
| MEDIUM | backend/cli/test/provider/managed-routing.test.ts | 60 | // ── Pure decision helpers ──────────────────────────────────────────────────── | COMMENT |
| MEDIUM | backend/cli/test/provider/managed-routing.test.ts | 121 | // ── Availability filter (hermetic, catalog-backed) ─────────────────────────── | COMMENT |
| MEDIUM | backend/cli/test/provider/managed-routing.test.ts | 468 | // ── billing.llm gates the own-key vs managed-proxy route (1a/1b/1c) ───────── | COMMENT |
| MEDIUM | backend/cli/test/provider/managed-routing.test.ts | 845 | // ── the invalidation must precede the announcement, not follow it ──────────── | COMMENT |
| MEDIUM⚡ | …/chemistry/molecular-docking/scripts/prepare_target.py | 350 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM⚡ | …/chemistry/molecular-docking/scripts/prepare_target.py | 352 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …/chemistry/molecular-docking/scripts/prepare_target.py | 23 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …/chemistry/molecular-docking/scripts/prepare_target.py | 25 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …/chemistry/molecular-docking/scripts/prepare_target.py | 57 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …/chemistry/molecular-docking/scripts/prepare_target.py | 59 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …/chemistry/molecular-docking/scripts/prepare_target.py | 70 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …/chemistry/molecular-docking/scripts/prepare_target.py | 72 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …/chemistry/molecular-docking/scripts/prepare_target.py | 99 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …/chemistry/molecular-docking/scripts/prepare_target.py | 101 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …/chemistry/molecular-docking/scripts/prepare_target.py | 325 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …/chemistry/molecular-docking/scripts/prepare_target.py | 327 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …/chemistry/molecular-docking/scripts/prepare_target.py | 532 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …/chemistry/molecular-docking/scripts/prepare_target.py | 534 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …chemistry/molecular-docking/scripts/prepare_ligands.py | 23 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …chemistry/molecular-docking/scripts/prepare_ligands.py | 25 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …chemistry/molecular-docking/scripts/prepare_ligands.py | 42 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …chemistry/molecular-docking/scripts/prepare_ligands.py | 44 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …chemistry/molecular-docking/scripts/prepare_ligands.py | 250 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …chemistry/molecular-docking/scripts/prepare_ligands.py | 252 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …chemistry/molecular-docking/scripts/prepare_ligands.py | 355 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …chemistry/molecular-docking/scripts/prepare_ligands.py | 357 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM⚡ | …cli/skills/chemistry/molecular-docking/scripts/dock.py | 74 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM⚡ | …cli/skills/chemistry/molecular-docking/scripts/dock.py | 76 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …cli/skills/chemistry/molecular-docking/scripts/dock.py | 28 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …cli/skills/chemistry/molecular-docking/scripts/dock.py | 30 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …cli/skills/chemistry/molecular-docking/scripts/dock.py | 140 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …cli/skills/chemistry/molecular-docking/scripts/dock.py | 142 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …cli/skills/chemistry/molecular-docking/scripts/dock.py | 536 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …cli/skills/chemistry/molecular-docking/scripts/dock.py | 538 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …cli/skills/chemistry/molecular-docking/scripts/dock.py | 806 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …cli/skills/chemistry/molecular-docking/scripts/dock.py | 808 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …cli/skills/chemistry/molecular-docking/scripts/dock.py | 904 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …cli/skills/chemistry/molecular-docking/scripts/dock.py | 906 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …cli/skills/chemistry/molecular-docking/scripts/rank.py | 30 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …cli/skills/chemistry/molecular-docking/scripts/rank.py | 32 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …cli/skills/chemistry/molecular-docking/scripts/rank.py | 184 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …cli/skills/chemistry/molecular-docking/scripts/rank.py | 186 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …cli/skills/chemistry/molecular-docking/scripts/rank.py | 313 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …cli/skills/chemistry/molecular-docking/scripts/rank.py | 315 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …cli/skills/chemistry/molecular-docking/scripts/rank.py | 370 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …cli/skills/chemistry/molecular-docking/scripts/rank.py | 372 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …cli/skills/chemistry/molecular-docking/scripts/rank.py | 466 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …cli/skills/chemistry/molecular-docking/scripts/rank.py | 468 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM⚡ | …li/skills/chemistry/molecular-docking/scripts/score.py | 496 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM⚡ | …li/skills/chemistry/molecular-docking/scripts/score.py | 498 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …li/skills/chemistry/molecular-docking/scripts/score.py | 25 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …li/skills/chemistry/molecular-docking/scripts/score.py | 27 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …li/skills/chemistry/molecular-docking/scripts/score.py | 59 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …li/skills/chemistry/molecular-docking/scripts/score.py | 61 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | …li/skills/chemistry/molecular-docking/scripts/score.py | 399 | # --------------------------------------------------------------------------- | COMMENT |
| 596 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | backend/cli/test/agent/harness-contract.test.ts | 210 | expect(skill).not.toContain("### Step 5: Save Report") | CODE |
| LOW | …earch/perplexity-search/references/openrouter_setup.md | 19 | ### Step 1: Create OpenRouter Account | COMMENT |
| LOW | …earch/perplexity-search/references/openrouter_setup.md | 26 | ### Step 2: Add Payment Method | COMMENT |
| LOW | …earch/perplexity-search/references/openrouter_setup.md | 41 | ### Step 3: Generate API Key | COMMENT |
| LOW | …earch/perplexity-search/references/openrouter_setup.md | 57 | ### Step 4: Configure Environment | COMMENT |
| LOW | …earch/perplexity-search/references/openrouter_setup.md | 123 | ### Step 5: Install Dependencies | COMMENT |
| LOW | …earch/perplexity-search/references/openrouter_setup.md | 145 | ### Step 6: Verify Setup | COMMENT |
| LOW | …earch/perplexity-search/references/openrouter_setup.md | 164 | ### Step 7: Test Your First Search | COMMENT |
| LOW | …lm-tools/huggingface-tokenizers/references/training.md | 7 | ### Step 1: Choose tokenization algorithm | COMMENT |
| LOW | …lm-tools/huggingface-tokenizers/references/training.md | 14 | ### Step 2: Prepare training data | COMMENT |
| LOW | …lm-tools/huggingface-tokenizers/references/training.md | 37 | ### Step 3: Initialize tokenizer | COMMENT |
| LOW | …lm-tools/huggingface-tokenizers/references/training.md | 94 | ### Step 4: Train | COMMENT |
| LOW | …lm-tools/huggingface-tokenizers/references/training.md | 114 | ### Step 5: Add post-processing | COMMENT |
| LOW | …lm-tools/huggingface-tokenizers/references/training.md | 138 | ### Step 6: Save | COMMENT |
| LOW | …/skills/llm-tools/sentencepiece/references/training.md | 7 | ### Step 1: Prepare corpus | COMMENT |
| LOW | …/skills/llm-tools/sentencepiece/references/training.md | 19 | ### Step 2: Train model | COMMENT |
| LOW | …/skills/llm-tools/sentencepiece/references/training.md | 45 | ### Step 3: Load and use | COMMENT |
| LOW | …i/skills/llm-tools/transformers/references/training.md | 9 | ### Step 1: Load and Preprocess Data | COMMENT |
| LOW | …i/skills/llm-tools/transformers/references/training.md | 36 | ### Step 2: Load Model | COMMENT |
| LOW | …i/skills/llm-tools/transformers/references/training.md | 47 | ### Step 3: Define Metrics | COMMENT |
| LOW | …i/skills/llm-tools/transformers/references/training.md | 61 | ### Step 4: Configure Training | COMMENT |
| LOW | …i/skills/llm-tools/transformers/references/training.md | 82 | ### Step 5: Create Trainer and Train | COMMENT |
| LOW | …i/skills/llm-tools/transformers/references/training.md | 103 | ### Step 6: Save Model | COMMENT |
| LOW⚡ | …kills/llm-tools/long-context/references/fine_tuning.md | 488 | # Step 1: 2k → 8k | COMMENT |
| LOW⚡ | …kills/llm-tools/long-context/references/fine_tuning.md | 491 | # Step 2: 8k → 16k | COMMENT |
| LOW⚡ | …kills/llm-tools/long-context/references/fine_tuning.md | 494 | # Step 3: 16k → 32k | COMMENT |
| LOW⚡ | backend/cli/skills/databases/kegg-database/SKILL.md | 214 | # Step 1: Find gene ID by name | COMMENT |
| LOW⚡ | backend/cli/skills/databases/kegg-database/SKILL.md | 217 | # Step 2: Link gene to pathways | COMMENT |
| LOW⚡ | backend/cli/skills/databases/kegg-database/SKILL.md | 220 | # Step 3: Get detailed pathway information | COMMENT |
| LOW | backend/cli/skills/databases/kegg-database/SKILL.md | 235 | # Step 1: List all human pathways | COMMENT |
| LOW | backend/cli/skills/databases/kegg-database/SKILL.md | 238 | # Step 2: For each pathway, get associated genes | COMMENT |
| LOW⚡ | backend/cli/skills/databases/kegg-database/SKILL.md | 253 | # Step 1: Search for compound | COMMENT |
| LOW⚡ | backend/cli/skills/databases/kegg-database/SKILL.md | 256 | # Step 2: Link compound to reactions | COMMENT |
| LOW⚡ | backend/cli/skills/databases/kegg-database/SKILL.md | 259 | # Step 3: Link reactions to pathways | COMMENT |
| LOW⚡ | backend/cli/skills/databases/kegg-database/SKILL.md | 262 | # Step 4: Get pathway details | COMMENT |
| LOW⚡ | backend/cli/skills/databases/kegg-database/SKILL.md | 273 | # Step 1: Convert KEGG gene IDs to external database IDs | COMMENT |
| LOW⚡ | backend/cli/skills/databases/kegg-database/SKILL.md | 277 | # Step 2: Parse conversion results | COMMENT |
| LOW⚡ | backend/cli/skills/databases/kegg-database/SKILL.md | 283 | # Step 3: Get sequences using KEGG | COMMENT |
| LOW⚡ | backend/cli/skills/databases/kegg-database/SKILL.md | 294 | # Step 1: List pathways for multiple organisms | COMMENT |
| LOW⚡ | backend/cli/skills/databases/kegg-database/SKILL.md | 299 | # Step 2: Get reference pathway for comparison | COMMENT |
| LOW⚡ | backend/cli/skills/databases/kegg-database/SKILL.md | 302 | # Step 3: Get organism-specific versions | COMMENT |
| LOW | …s/databases/cosmic-database/scripts/download_cosmic.py | 64 | # Step 1: Get the download URL | COMMENT |
| LOW⚡ | …s/databases/cosmic-database/scripts/download_cosmic.py | 91 | # Step 2: Download the file | COMMENT |
| LOW⚡ | …s/databases/cosmic-database/scripts/download_cosmic.py | 99 | # Step 3: Write to disk | COMMENT |
| LOW | …skills/databases/fred-economic-data/references/tags.md | 411 | # Step 1: Find tags matching the topic | COMMENT |
| LOW | …skills/databases/fred-economic-data/references/tags.md | 428 | # Step 2: Find related tags | COMMENT |
| LOW | backend/cli/skills/databases/geo-database/SKILL.md | 261 | # Step 1: Search for GEO entries | COMMENT |
| LOW | backend/cli/skills/databases/geo-database/SKILL.md | 274 | # Step 2: Fetch summaries | COMMENT |
| LOW | backend/cli/skills/databases/geo-database/SKILL.md | 283 | # Step 3: Fetch full records | COMMENT |
| LOW⚡ | …databases/clinvar-database/references/api_reference.md | 121 | # Step 1: Search for variants | COMMENT |
| LOW⚡ | …databases/clinvar-database/references/api_reference.md | 124 | # Step 2: Parse IDs from search results | COMMENT |
| LOW⚡ | …databases/clinvar-database/references/api_reference.md | 127 | # Step 3: Retrieve summaries | COMMENT |
| LOW⚡ | …databases/clinvar-database/references/api_reference.md | 130 | # Step 4: Fetch full records if needed | COMMENT |
| LOW⚡ | …databases/pubchem-database/references/api_reference.md | 154 | # Step 1: Submit similarity search | COMMENT |
| LOW⚡ | …databases/pubchem-database/references/api_reference.md | 161 | # Step 2: Check status | COMMENT |
| LOW⚡ | …databases/pubchem-database/references/api_reference.md | 164 | # Step 3: Poll until ready (with timeout) | COMMENT |
| LOW⚡ | …databases/pubchem-database/references/api_reference.md | 165 | # Step 4: Retrieve results from the same URL | COMMENT |
| LOW⚡ | …atabases/pubchem-database/scripts/bioactivity_query.py | 307 | # Step 1: Find assays for the target | COMMENT |
| LOW⚡ | …atabases/pubchem-database/scripts/bioactivity_query.py | 314 | # Step 2: Get active compounds from these assays | COMMENT |
| LOW⚡ | backend/cli/skills/databases/string-database/SKILL.md | 281 | # Step 1: Map gene names to STRING IDs | COMMENT |
| 705 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| MEDIUM | backend/cli/skills/research/perplexity-search/SKILL.md | 211 | print(f"Error: {result['error']}") | CODE |
| LOW | …skills/research/perplexity-search/scripts/setup_env.py | 56 | except Exception as e: | CODE |
| MEDIUM | …skills/research/perplexity-search/scripts/setup_env.py | 57 | print(f"Error creating .env file: {e}", file=sys.stderr) | CODE |
| MEDIUM⚡ | …esearch/perplexity-search/scripts/perplexity_search.py | 32 | print("Error: LiteLLM is not installed.", file=sys.stderr) | CODE |
| MEDIUM⚡ | …esearch/perplexity-search/scripts/perplexity_search.py | 41 | print("Error: OPENROUTER_API_KEY environment variable is not set.", file=sys.stderr) | CODE |
| LOW | …esearch/perplexity-search/scripts/perplexity_search.py | 126 | except Exception as e: | CODE |
| MEDIUM | …esearch/perplexity-search/scripts/perplexity_search.py | 250 | print(f"Error: {result['error']}", file=sys.stderr) | STRING |
| LOW | …cli/skills/research/research-lookup/research_lookup.py | 251 | except Exception as e: | CODE |
| LOW | …cli/skills/research/research-lookup/research_lookup.py | 354 | except Exception as e: | CODE |
| MEDIUM | …cli/skills/research/research-lookup/research_lookup.py | 391 | print("Error: OPENROUTER_API_KEY environment variable not set", file=sys.stderr) | CODE |
| MEDIUM | …cli/skills/research/research-lookup/research_lookup.py | 413 | print("Error: No query provided. Use --model-info to see available models.", file=sys.stderr) | CODE |
| LOW | …cli/skills/research/research-lookup/research_lookup.py | 475 | except Exception as e: | CODE |
| MEDIUM | …cli/skills/research/research-lookup/research_lookup.py | 476 | print(f"Error: {str(e)}", file=sys.stderr) | CODE |
| LOW | backend/cli/skills/research/research-lookup/lookup.py | 181 | except Exception as e: | CODE |
| LOW | …ls/research/research-lookup/scripts/research_lookup.py | 251 | except Exception as e: | CODE |
| LOW | …ls/research/research-lookup/scripts/research_lookup.py | 354 | except Exception as e: | CODE |
| MEDIUM | …ls/research/research-lookup/scripts/research_lookup.py | 391 | print("Error: OPENROUTER_API_KEY environment variable not set", file=sys.stderr) | CODE |
| MEDIUM | …ls/research/research-lookup/scripts/research_lookup.py | 413 | print("Error: No query provided. Use --model-info to see available models.", file=sys.stderr) | CODE |
| LOW | …ls/research/research-lookup/scripts/research_lookup.py | 475 | except Exception as e: | CODE |
| MEDIUM | …ls/research/research-lookup/scripts/research_lookup.py | 476 | print(f"Error: {str(e)}", file=sys.stderr) | CODE |
| LOW | …et-research-reports/scripts/generate_market_visuals.py | 361 | except Exception as e: | CODE |
| LOW | …ualization/scientific-schematics/test_ai_generation.py | 76 | except Exception as e: | CODE |
| LOW | …ualization/scientific-schematics/test_ai_generation.py | 109 | except Exception as e: | CODE |
| LOW | …ualization/scientific-schematics/test_ai_generation.py | 129 | except Exception as e: | CODE |
| LOW | …ualization/scientific-schematics/test_ai_generation.py | 168 | except Exception as e: | CODE |
| LOW | …ualization/scientific-schematics/test_ai_generation.py | 212 | except Exception as e: | CODE |
| MEDIUM | …scientific-schematics/scripts/generate_schematic_ai.py | 34 | print("Error: requests library not found. Install with: pip install requests") | CODE |
| LOW | …scientific-schematics/scripts/generate_schematic_ai.py | 324 | except Exception as e: | CODE |
| LOW | …scientific-schematics/scripts/generate_schematic_ai.py | 417 | except Exception as e: | CODE |
| LOW | …scientific-schematics/scripts/generate_schematic_ai.py | 588 | except Exception as e: | CODE |
| MEDIUM | …scientific-schematics/scripts/generate_schematic_ai.py | 821 | print("Error: Iterations must be between 1 and 2") | STRING |
| LOW | …scientific-schematics/scripts/generate_schematic_ai.py | 840 | except Exception as e: | STRING |
| MEDIUM | …on/scientific-schematics/scripts/generate_schematic.py | 99 | print(f"Error: AI generation script not found: {ai_script}") | STRING |
| LOW | …on/scientific-schematics/scripts/generate_schematic.py | 123 | except Exception as e: | STRING |
| MEDIUM | …on/scientific-schematics/scripts/generate_schematic.py | 124 | print(f"Error executing AI generation: {e}") | STRING |
| MEDIUM | …ualization/protein-diagram/scripts/draw_contact_map.py | 20 | print("Error: BioPython is required. Install with: pip install biopython", file=sys.stderr) | CODE |
| MEDIUM | …ualization/protein-diagram/scripts/draw_contact_map.py | 75 | print(f"Error: No C-alpha atoms found for chain {args.chain}.", file=sys.stderr) | CODE |
| MEDIUM | …isualization/protein-diagram/scripts/draw_alignment.py | 20 | print("Error: pyMSAviz is required. Install with: pip install pymsaviz", file=sys.stderr) | CODE |
| MEDIUM | …on/protein-diagram/scripts/draw_secondary_structure.py | 20 | print("Error: BioPython is required. Install with: pip install biopython", file=sys.stderr) | CODE |
| LOW⚡ | …on/protein-diagram/scripts/draw_secondary_structure.py | 55 | except Exception: | CODE |
| LOW⚡ | …on/protein-diagram/scripts/draw_secondary_structure.py | 58 | except Exception as e: | CODE |
| MEDIUM⚡ | …on/protein-diagram/scripts/draw_secondary_structure.py | 59 | print(f"Error running DSSP: {e}", file=sys.stderr) | CODE |
| MEDIUM | …on/protein-diagram/scripts/draw_secondary_structure.py | 78 | print("Error: No residues found for specified chain.", file=sys.stderr) | CODE |
| MEDIUM | …visualization/protein-diagram/scripts/draw_features.py | 52 | print(f"Error fetching UniProt data for {uniprot_id}: {e}", file=sys.stderr) | CODE |
| MEDIUM | …visualization/protein-diagram/scripts/draw_features.py | 92 | print(f"Error: Cannot parse features from '{features_arg}'.", file=sys.stderr) | CODE |
| MEDIUM | …visualization/protein-diagram/scripts/draw_features.py | 123 | print("Error: Provide either --uniprot or --features.", file=sys.stderr) | CODE |
| MEDIUM | …sualization/protein-diagram/scripts/draw_domain_map.py | 41 | print(f"Error fetching InterPro data for {uniprot_id}: {e}", file=sys.stderr) | CODE |
| LOW | …sualization/protein-diagram/scripts/draw_domain_map.py | 51 | except Exception: | CODE |
| MEDIUM | …sualization/protein-diagram/scripts/draw_domain_map.py | 84 | print(f"Error: Cannot parse domains from '{domains_arg}'. Provide a JSON file or inline JSON array.", | CODE |
| MEDIUM | …sualization/protein-diagram/scripts/draw_domain_map.py | 171 | print("Error: Could not determine protein length. Provide --length.", file=sys.stderr) | CODE |
| MEDIUM | …sualization/protein-diagram/scripts/draw_domain_map.py | 181 | print("Error: Provide either --uniprot or --domains.", file=sys.stderr) | CODE |
| MEDIUM | …alization/protein-diagram/scripts/draw_ramachandran.py | 22 | print("Error: BioPython is required. Install with: pip install biopython", file=sys.stderr) | CODE |
| MEDIUM | …alization/protein-diagram/scripts/draw_ramachandran.py | 95 | print("Error: No phi/psi angles found. Check PDB file and chain ID.", file=sys.stderr) | CODE |
| MEDIUM | …zation/infographics/scripts/generate_infographic_ai.py | 35 | print("Error: requests library not found. Install with: pip install requests") | CODE |
| LOW | …zation/infographics/scripts/generate_infographic_ai.py | 286 | except Exception: | STRING |
| LOW | …zation/infographics/scripts/generate_infographic_ai.py | 504 | except Exception as e: | CODE |
| LOW | …zation/infographics/scripts/generate_infographic_ai.py | 578 | except Exception as e: | CODE |
| LOW | …zation/infographics/scripts/generate_infographic_ai.py | 706 | except Exception as e: | CODE |
| LOW | …zation/infographics/scripts/generate_infographic_ai.py | 808 | except Exception as e: | CODE |
| LOW | …zation/infographics/scripts/generate_infographic_ai.py | 959 | except Exception as e: | CODE |
| 822 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| HIGH⚡ | …esearch/perplexity-search/scripts/perplexity_search.py | 45 | print(" export OPENROUTER_API_KEY='your-api-key-here'", file=sys.stderr) | CODE |
| HIGH⚡ | …esearch/perplexity-search/scripts/perplexity_search.py | 47 | print(" OPENROUTER_API_KEY=your-api-key-here", file=sys.stderr) | CODE |
| HIGH | …zation/infographics/scripts/generate_infographic_ai.py | 1284 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH⚡ | …alization/infographics/scripts/generate_infographic.py | 182 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH | backend/cli/skills/llm-tools/dspy/SKILL.md | 293 | api_key="your-api-key", # Or set ANTHROPIC_API_KEY env var | CODE |
| HIGH | backend/cli/skills/llm-tools/dspy/SKILL.md | 305 | api_key="your-api-key", | CODE |
| HIGH | backend/cli/skills/llm-tools/langsmith/SKILL.md | 46 | export LANGSMITH_API_KEY="your-api-key" | CODE |
| HIGH⚡ | …ills/llm-tools/langsmith/references/troubleshooting.md | 45 | export LANGSMITH_API_KEY="your-api-key" | CODE |
| HIGH⚡ | …ills/llm-tools/langsmith/references/troubleshooting.md | 48 | LANGSMITH_API_KEY=your-api-key | CODE |
| HIGH⚡ | …ills/llm-tools/langsmith/references/troubleshooting.md | 55 | client = Client(api_key="your-api-key") | CODE |
| HIGH | backend/cli/skills/llm-tools/langchain/SKILL.md | 340 | os.environ["LANGCHAIN_API_KEY"] = "your-api-key" | CODE |
| HIGH | …i/skills/llm-tools/langchain/references/integration.md | 40 | pinecone.init(api_key="your-api-key", environment="us-west1-gcp") | CODE |
| HIGH | backend/cli/skills/llm-tools/guidance/SKILL.md | 273 | api_key="your-api-key" # Or set ANTHROPIC_API_KEY env var | CODE |
| HIGH | backend/cli/skills/llm-tools/guidance/SKILL.md | 282 | api_key="your-api-key" # Or set OPENAI_API_KEY env var | CODE |
| HIGH | …d/cli/skills/llm-tools/guidance/references/backends.md | 28 | api_key="your-api-key-here" | CODE |
| HIGH | …d/cli/skills/llm-tools/guidance/references/backends.md | 53 | api_key="your-api-key", | CODE |
| HIGH | …d/cli/skills/llm-tools/guidance/references/backends.md | 95 | api_key="your-api-key-here" | CODE |
| HIGH | …d/cli/skills/llm-tools/guidance/references/backends.md | 120 | api_key="your-api-key", | CODE |
| HIGH | backend/cli/skills/llm-tools/pinecone/SKILL.md | 51 | pc = Pinecone(api_key="your-api-key") | CODE |
| HIGH | backend/cli/skills/llm-tools/qdrant/SKILL.md | 419 | api_key="your-api-key" | CODE |
| HIGH | …/skills/llm-tools/qdrant/references/troubleshooting.md | 117 | api_key="your-api-key" | CODE |
| HIGH | …lls/llm-tools/generate-image/scripts/generate_image.py | 125 | print("or set it for this run: export OPENROUTER_API_KEY=your-api-key-here.") | CODE |
| HIGH | backend/cli/skills/llm-tools/outlines/SKILL.md | 225 | api_key="your-api-key" | CODE |
| HIGH | …d/cli/skills/llm-tools/outlines/references/backends.md | 381 | model = outlines.models.openai("gpt-4o-mini", api_key="your-api-key") | CODE |
| HIGH | …d/cli/skills/llm-tools/outlines/references/backends.md | 393 | api_key="your-api-key", # Or set OPENAI_API_KEY env var | CODE |
| HIGH | backend/cli/skills/llm-tools/instructor/SKILL.md | 342 | Anthropic(api_key="your-api-key") | CODE |
| HIGH | backend/cli/skills/llm-tools/instructor/SKILL.md | 360 | OpenAI(api_key="your-api-key") | CODE |
| HIGH | …li/skills/llm-tools/instructor/references/providers.md | 16 | Anthropic(api_key="your-api-key") | CODE |
| HIGH | backend/cli/skills/databases/uspto-database/SKILL.md | 156 | "X-Api-Key": "YOUR_API_KEY", | CODE |
| HIGH | …s/databases/uspto-database/references/trademark_api.md | 26 | X-Api-Key: YOUR_API_KEY | CODE |
| HIGH | …s/databases/uspto-database/references/trademark_api.md | 123 | data = get_trademark_status("87654321", "YOUR_API_KEY") | CODE |
| HIGH | …s/databases/uspto-database/references/trademark_api.md | 147 | X-Api-Key: YOUR_API_KEY | CODE |
| HIGH | …s/databases/uspto-database/references/trademark_api.md | 240 | xml_data = search_trademark_assignments("5678901", "YOUR_API_KEY") | CODE |
| HIGH | …atabases/uspto-database/references/patentsearch_api.md | 14 | X-Api-Key: YOUR_API_KEY | CODE |
| HIGH | …atabases/uspto-database/references/patentsearch_api.md | 177 | -H "X-Api-Key: YOUR_API_KEY" \ | CODE |
| HIGH | …atabases/uspto-database/references/patentsearch_api.md | 199 | "X-Api-Key": "YOUR_API_KEY", | CODE |
| HIGH | …ls/databases/gene-database/references/api_reference.md | 191 | api-key: YOUR_API_KEY | CODE |
| HIGH | …/databases/drugbank-database/references/data-access.md | 149 | headers = {"Authorization": "Bearer YOUR_API_KEY"} | CODE |
| HIGH | backend/cli/skills/databases/fda-database/SKILL.md | 45 | fda = FDAQuery(api_key="YOUR_API_KEY") | CODE |
| HIGH | …databases/fda-database/references/animal_veterinary.md | 93 | api_key = "YOUR_API_KEY" | CODE |
| HIGH | …li/skills/databases/fda-database/references/devices.md | 53 | api_key = "YOUR_API_KEY" | CODE |
| HIGH | …/cli/skills/databases/fda-database/references/foods.md | 54 | api_key = "YOUR_API_KEY" | CODE |
| HIGH | …/cli/skills/databases/fda-database/references/drugs.md | 39 | api_key = "YOUR_API_KEY" | CODE |
| HIGH | …/cli/skills/databases/fda-database/references/other.md | 81 | api_key = "YOUR_API_KEY" | CODE |
| HIGH | …cli/skills/databases/fda-database/scripts/fda_query.py | 11 | fda = FDAQuery(api_key="YOUR_API_KEY") | STRING |
| HIGH⚡ | backend/cli/skills/databases/pubmed-database/SKILL.md | 136 | "api_key": "YOUR_API_KEY" # Optional but recommended | CODE |
| HIGH⚡ | backend/cli/skills/databases/pubmed-database/SKILL.md | 148 | "api_key": "YOUR_API_KEY" | CODE |
| HIGH | …/databases/pubmed-database/references/api_reference.md | 17 | esearch.fcgi?db=pubmed&term=cancer&api_key=YOUR_API_KEY | CODE |
| HIGH | …/databases/pubmed-database/references/api_reference.md | 51 | esearch.fcgi?db=pubmed&term=breast+cancer&retmax=100&retmode=json&api_key=YOUR_API_KEY | CODE |
| HIGH | …/databases/pubmed-database/references/api_reference.md | 80 | efetch.fcgi?db=pubmed&id=123456,234567&rettype=abstract&retmode=text&api_key=YOUR_API_KEY | CODE |
| HIGH | …/databases/pubmed-database/references/api_reference.md | 105 | esummary.fcgi?db=pubmed&id=123456,234567&retmode=json&version=2.0&api_key=YOUR_API_KEY | CODE |
| HIGH | …/databases/pubmed-database/references/api_reference.md | 129 | epost.fcgi?db=pubmed&id=123456,234567,345678&api_key=YOUR_API_KEY | CODE |
| HIGH | …/databases/pubmed-database/references/api_reference.md | 154 | elink.fcgi?dbfrom=pubmed&db=pubmed&id=123456&cmd=neighbor&api_key=YOUR_API_KEY | CODE |
| HIGH | …/databases/pubmed-database/references/api_reference.md | 175 | einfo.fcgi?db=pubmed&retmode=json&api_key=YOUR_API_KEY | CODE |
| HIGH | …/databases/pubmed-database/references/api_reference.md | 195 | egquery.fcgi?term=cancer&api_key=YOUR_API_KEY | CODE |
| HIGH | …/databases/pubmed-database/references/api_reference.md | 210 | espell.fcgi?db=pubmed&term=cancre&api_key=YOUR_API_KEY | CODE |
| HIGH⚡ | …/databases/pubmed-database/references/api_reference.md | 242 | esearch.fcgi?db=pubmed&term=cancer&usehistory=y&retmode=json&api_key=YOUR_API_KEY | CODE |
| HIGH⚡ | …/databases/pubmed-database/references/api_reference.md | 247 | efetch.fcgi?db=pubmed&query_key=1&WebEnv=MCID_12345&retstart=0&retmax=500&rettype=xml&api_key=YOUR_API_KEY | CODE |
| HIGH⚡ | …/databases/pubmed-database/references/api_reference.md | 248 | efetch.fcgi?db=pubmed&query_key=1&WebEnv=MCID_12345&retstart=500&retmax=500&rettype=xml&api_key=YOUR_API_KEY | CODE |
| HIGH⚡ | …/databases/pubmed-database/references/api_reference.md | 257 | epost.fcgi?db=pubmed&id=123,456,789,...&api_key=YOUR_API_KEY | CODE |
| 29 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | tooling/repo/npm-release.ts | 119 | export function nativeReleasePackageNames() { | CODE |
| LOW | tooling/repo/npm-release.ts | 201 | export function createCompiledPackageManifest( | CODE |
| LOW | tooling/repo/npm-release.ts | 363 | export async function verifyPackedModuleExports( | CODE |
| LOW | tooling/repo/npm-release.ts | 524 | export async function verifyPublishedPackageIntegrities(inputs: PackedPackage[], options: NpmCommandOptions = {}) { | CODE |
| LOW | tooling/repo/npm-release.ts | 531 | async function submitCandidatePackageOnce( | CODE |
| LOW | tooling/repo/npm-release.ts | 574 | export async function assertReleaseVersionUnoccupied(version: string, options: NpmCommandOptions = {}) { | CODE |
| LOW | tooling/repo/npm-release.ts | 596 | export async function verifyReleaseOptionalDependencies(artifacts: PackedPackage[], options: NpmCommandOptions = {}) { | CODE |
| LOW | evals/cadence-harness/tree-metrics.ts | 98 | export function aggregateCapturedSessionTree( | CODE |
| LOW | frontend/ui/src/context/marked.tsx | 403 | export function registerOpenScienceDiffTheme(diffs: Pick<DiffsModule, "registerCustomTheme">) { | CODE |
| LOW | frontend/ui/src/components/dropdown-menu.tsx | 182 | function DropdownMenuItemDescription(props: ParentProps<DropdownMenuItemDescriptionProps>) { | CODE |
| LOW | frontend/ui/src/components/dropdown-menu.tsx | 198 | function DropdownMenuItemIndicator(props: ParentProps<DropdownMenuItemIndicatorProps>) { | CODE |
| LOW | frontend/ui/src/theme/resolve.ts | 300 | function generateNeutralAlphaScale(neutralScale: HexColor[], isDark: boolean): HexColor[] { | CODE |
| LOW | frontend/workspace/script/e2e-mode.ts | 62 | export function externalRunnerEnvironment(env: Environment, packaged = false): Record<string, string> { | CODE |
| LOW | frontend/workspace/src/artifacts/bytes.ts | 15 | export function storedArtifactPreviewKind(version: StoredArtifactVersion): StoredArtifactPreview["kind"] | undefined { | CODE |
| LOW | frontend/workspace/src/artifacts/bytes.ts | 51 | export async function loadStoredArtifactPreview( | CODE |
| LOW | …ontend/workspace/src/artifacts/stored-artifact-menu.ts | 3 | export function moveStoredArtifactMenuFocus(scope: HTMLElement, target: EventTarget | null, key: string) { | CODE |
| LOW | frontend/workspace/src/artifacts/inspector.ts | 158 | export function normalizeHistoricalReviews(value: unknown): HistoricalReviewFinding[] { | CODE |
| LOW | frontend/workspace/src/artifacts/inspector.ts | 351 | export function normalizePublicationReview(format: string, value: unknown): PublicationReviewState { | CODE |
| LOW | frontend/workspace/src/artifacts/store.ts | 74 | export function normalizeStoredArtifactVersion(value: unknown): StoredArtifactVersion | undefined { | CODE |
| LOW | frontend/workspace/src/artifacts/store.ts | 108 | export function storedArtifactReviewTargetID(version: Pick<StoredArtifactVersion, "id" | "sha256">) { | CODE |
| LOW | frontend/workspace/src/artifacts/store.ts | 154 | export function normalizeStoredArtifactDetail(value: unknown): StoredArtifactDetail | undefined { | CODE |
| LOW | frontend/workspace/src/context/session-hydration.ts | 54 | export function nextReconnectHydrationLimit(input: { limit: number; snapshotCount: number; overlapsCached: boolean }) { | CODE |
| LOW | frontend/workspace/src/context/session-hydration.ts | 60 | export function createReconnectGenerationGuard() { | CODE |
| LOW | frontend/workspace/src/context/terminal.tsx | 29 | function createProjectTerminalSession( | CODE |
| LOW | frontend/workspace/src/context/permission.tsx | 40 | function hasAutoAcceptPermissionConfig(permission: unknown) { | CODE |
| LOW | frontend/workspace/src/science/formats/binary.ts | 33 | export function detectBinaryScienceFormat(extension: string): BinaryScienceFormat | undefined { | CODE |
| LOW | frontend/workspace/src/utils/stale-build-recovery.ts | 20 | export function installStaleBuildRecovery(options: StaleBuildRecoveryOptions = {}): () => void { | CODE |
| LOW | frontend/workspace/src/utils/native-picker.ts | 18 | export async function openNativeDirectoryPicker( | CODE |
| LOW | …ontend/workspace/src/components/prompt-capabilities.ts | 62 | export function publishCapabilityPreferences(preferences: CapabilityPreferences) { | CODE |
| LOW | frontend/workspace/src/components/prompt-submission.ts | 8 | export function canRestoreFailedSubmission(current: Prompt, mode: "normal" | "shell") { | CODE |
| LOW | …nd/workspace/src/components/model-settings-popover.tsx | 55 | export function modelRadioNavigationTarget(scope: HTMLElement, target: EventTarget | null, key: string) { | CODE |
| LOW | …pace/src/components/settings/scientific-tools-state.ts | 78 | export function filterScientificCapabilities( | CODE |
| LOW | …nd/workspace/src/components/settings/connector-form.ts | 71 | export function connectorMatchesCatalogSetup( | CODE |
| LOW | frontend/workspace/src/atlas/skill-permissions.ts | 54 | export function restoreExactSkillPermission(current: unknown, before: unknown, name: string) { | CODE |
| LOW | frontend/workspace/src/atlas/file-viewer.ts | 78 | export function isFileRequestCancellation(error: unknown) { | CODE |
| LOW | frontend/workspace/src/atlas/kernel-api.ts | 57 | export function createKernelRouteRequester(request: KernelTransport) { | CODE |
| LOW | frontend/workspace/src/atlas/file-sources.ts | 158 | export function connectedFilesystemGrants(snapshot?: FilesystemSnapshot) { | CODE |
| LOW | …pace/src/atlas/project-workspace-lifecycle.fixture.tsx | 5 | export function mountProjectWorkspaceLifecycle(host: HTMLElement) { | CODE |
| LOW | frontend/workspace/src/atlas/terminal-endpoint.ts | 3 | export function terminalEndpointAvailable(value: string, origin?: string) { | CODE |
| LOW | frontend/workspace/src/atlas/session-trace-model.ts | 163 | export function fallbackObservableKernels( | CODE |
| LOW | frontend/workspace/src/atlas/ExecutionHistoryAPI.ts | 91 | export function createExecutionHistoryAPI(request: RequestTransport) { | CODE |
| LOW | frontend/workspace/src/atlas/execution-authority.ts | 71 | export function createExecutionAuthorityAPI(request: ProjectRequest) { | CODE |
| LOW | frontend/workspace/src/atlas/execution-authority.ts | 117 | export function executionAuthorityMessage(decision: ExecutionDecision): string | undefined { | CODE |
| LOW | backend/cli/script/encrypt-prompts-plugin.ts | 25 | export function createEncryptPromptsPlugin(keyFragments: string[]): { | CODE |
| LOW | backend/cli/script/publish-manifest.ts | 28 | export function assertPublicPackageSurface(files: Record<string, string>) { | CODE |
| LOW | backend/cli/script/publish-manifest.ts | 37 | export function createWrapperPackageManifest(options: WrapperPackageManifestOptions) { | CODE |
| LOW | …cli/skills/research/research-lookup/research_lookup.py | 300 | def _extract_citations_from_text(self, text: str) -> List[Dict[str, str]]: | CODE |
| LOW | backend/cli/skills/research/research-lookup/examples.py | 17 | def example_automatic_selection(): | CODE |
| LOW | backend/cli/skills/research/research-lookup/examples.py | 97 | def example_scientific_writing_workflow(): | CODE |
| LOW | …ls/research/research-lookup/scripts/research_lookup.py | 300 | def _extract_citations_from_text(self, text: str) -> List[Dict[str, str]]: | CODE |
| LOW | …scientific-schematics/scripts/generate_schematic_ai.py | 249 | def _extract_image_from_response(self, response: Dict[str, Any]) -> Optional[bytes]: | CODE |
| LOW | …zation/infographics/scripts/generate_infographic_ai.py | 582 | def _enhance_prompt_with_research(self, user_prompt: str, research_data: Dict[str, Any]) -> str: | CODE |
| LOW | …zation/infographics/scripts/generate_infographic_ai.py | 652 | def _extract_image_from_response(self, response: Dict[str, Any]) -> Optional[bytes]: | CODE |
| LOW | …ills/visualization/matplotlib/scripts/plot_template.py | 316 | def create_comprehensive_figure(): | CODE |
| LOW | backend/cli/skills/llm-tools/nemo-guardrails/SKILL.md | 97 | async def check_output_hallucination(context): | CODE |
| LOW | …i/skills/llm-tools/instructor/references/validation.md | 295 | def at_least_one_high_priority(cls, v): | CODE |
| LOW | …d/cli/skills/llm-tools/long-context/references/rope.md | 114 | def apply_rotary_pos_emb_gpt_neox(q, k, cos, sin, position_ids=None): | CODE |
| LOW | …llm-tools/long-context/references/extension_methods.md | 48 | def yarn_find_correction_range(low_rot, high_rot, dim, base=10000, max_position_embeddings=2048): | CODE |
| LOW | …kills/llm-tools/long-context/references/fine_tuning.md | 226 | def prepare_long_context_data(dataset, tokenizer, context_length=32768): | CODE |
| LOW | backend/cli/skills/databases/uspto-database/SKILL.md | 502 | def comprehensive_patent_analysis(patent_number, api_key): | CODE |
| 361 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| MEDIUM | frontend/landing/public/docs/assets/index-Cazmh0hf.js | 300 | `,T1='---\ntitle: "Local models"\ndescription: "Run OpenScience against a local LLM — Ollama, LM Studio, llama.cpp, vLLM | CODE |
| MEDIUM | backend/cli/AGENTS.md | 26 | ### RAG & Retrieval | COMMENT |
| MEDIUM | backend/cli/skills/llm-tools/dspy/SKILL.md | 252 | #### RAG System with Optimization | COMMENT |
| MEDIUM | …ckend/cli/skills/llm-tools/dspy/references/examples.md | 12 | ## RAG Systems | COMMENT |
| MEDIUM | …ckend/cli/skills/llm-tools/dspy/references/examples.md | 14 | ### Basic RAG | COMMENT |
| MEDIUM | …ckend/cli/skills/llm-tools/dspy/references/examples.md | 40 | # Use RAG | COMMENT |
| MEDIUM | …ckend/cli/skills/llm-tools/dspy/references/examples.md | 46 | ### Optimized RAG | COMMENT |
| MEDIUM⚡ | …ckend/cli/skills/llm-tools/dspy/references/examples.md | 65 | # Optimize RAG | COMMENT |
| MEDIUM⚡ | …ckend/cli/skills/llm-tools/dspy/references/examples.md | 69 | # Optimized RAG performs better on similar questions | COMMENT |
| MEDIUM⚡ | …ckend/cli/skills/llm-tools/dspy/references/examples.md | 73 | ### Multi-Hop RAG | COMMENT |
| MEDIUM | …ckend/cli/skills/llm-tools/dspy/references/examples.md | 105 | # Use multi-hop RAG | COMMENT |
| MEDIUM | …ckend/cli/skills/llm-tools/dspy/references/examples.md | 112 | ### RAG with Reranking | COMMENT |
| MEDIUM | …ckend/cli/skills/llm-tools/dspy/references/examples.md | 225 | # Use multi-agent system | COMMENT |
| MEDIUM | …end/cli/skills/llm-tools/dspy/references/optimizers.md | 71 | # Now optimized_qa has learned few-shot examples! | COMMENT |
| MEDIUM | …end/cli/skills/llm-tools/dspy/references/optimizers.md | 433 | # Stage 1: Bootstrap few-shot | COMMENT |
| MEDIUM | backend/cli/skills/llm-tools/nemo-guardrails/SKILL.md | 291 | - Docs: https://docs.nvidia.com/nemo/guardrails/ | STRING |
| MEDIUM | backend/cli/skills/llm-tools/llamaindex/SKILL.md | 53 | ### 5-line RAG example | COMMENT |
| MEDIUM | backend/cli/skills/llm-tools/llamaindex/SKILL.md | 194 | ### RAG agent (document search + tools) | COMMENT |
| MEDIUM | backend/cli/skills/llm-tools/llamaindex/SKILL.md | 219 | ## Advanced RAG patterns | COMMENT |
| MEDIUM | backend/cli/skills/llm-tools/llamaindex/SKILL.md | 422 | ## Multi-modal RAG | COMMENT |
| MEDIUM | backend/cli/skills/llm-tools/llamaindex/SKILL.md | 461 | # Evaluate faithfulness (no hallucination) | COMMENT |
| MEDIUM | backend/cli/skills/llm-tools/llamaindex/SKILL.md | 488 | # Complete RAG pipeline | COMMENT |
| MEDIUM | …kills/llm-tools/llamaindex/references/query_engines.md | 34 | # Combines chunks that fit in context window | COMMENT |
| MEDIUM | …kills/llm-tools/llamaindex/references/query_engines.md | 297 | # 2. context - Simple RAG | COMMENT |
| MEDIUM | …d/cli/skills/llm-tools/llamaindex/references/agents.md | 25 | ## RAG agent | COMMENT |
| MEDIUM | …d/cli/skills/llm-tools/llamaindex/references/agents.md | 39 | # Agent with RAG + calculator | COMMENT |
| MEDIUM | backend/cli/skills/llm-tools/crewai/SKILL.md | 375 | ## Flows - Event-driven orchestration | COMMENT |
| MEDIUM | …/skills/llm-tools/blip-2/references/troubleshooting.md | 354 | ### VQA hallucinations | COMMENT |
| MEDIUM | backend/cli/skills/llm-tools/langchain/SKILL.md | 12 | # LangChain - Build LLM Applications with Agents & RAG | COMMENT |
| MEDIUM | backend/cli/skills/llm-tools/langchain/SKILL.md | 184 | ## RAG (Retrieval-Augmented Generation) | COMMENT |
| MEDIUM | backend/cli/skills/llm-tools/langchain/SKILL.md | 186 | ### Basic RAG pipeline | COMMENT |
| MEDIUM⚡ | backend/cli/skills/llm-tools/langchain/SKILL.md | 228 | ### Conversational RAG with memory | COMMENT |
| MEDIUM⚡ | backend/cli/skills/llm-tools/langchain/SKILL.md | 233 | # RAG with conversation memory | COMMENT |
| MEDIUM⚡ | backend/cli/skills/llm-tools/langchain/SKILL.md | 243 | # Multi-turn RAG | COMMENT |
| MEDIUM | …ckend/cli/skills/llm-tools/langchain/references/rag.md | 1 | # LangChain RAG Guide | COMMENT |
| MEDIUM | …ckend/cli/skills/llm-tools/langchain/references/rag.md | 5 | ## What is RAG? | COMMENT |
| MEDIUM | …ckend/cli/skills/llm-tools/langchain/references/rag.md | 17 | ## RAG pipeline components | COMMENT |
| MEDIUM | …ckend/cli/skills/llm-tools/langchain/references/rag.md | 194 | ## Advanced RAG patterns | COMMENT |
| MEDIUM | …ckend/cli/skills/llm-tools/langchain/references/rag.md | 196 | ### Conversational RAG | COMMENT |
| MEDIUM | …ckend/cli/skills/llm-tools/langchain/references/rag.md | 209 | # Conversational RAG chain | COMMENT |
| MEDIUM | …ckend/cli/skills/llm-tools/langchain/references/rag.md | 341 | ## RAG with agents | COMMENT |
| MEDIUM | …ckend/cli/skills/llm-tools/langchain/references/rag.md | 343 | ### Agent-based RAG | COMMENT |
| MEDIUM | …ckend/cli/skills/llm-tools/langchain/references/rag.md | 582 | # Async RAG for concurrent queries | COMMENT |
| MEDIUM | …nd/cli/skills/llm-tools/langchain/references/agents.md | 160 | ### 2. ReAct agent (reasoning trace) | COMMENT |
| MEDIUM | …d/cli/skills/llm-tools/guidance/references/backends.md | 415 | # - Avoid large few-shot examples | COMMENT |
| MEDIUM | backend/cli/skills/llm-tools/qdrant/SKILL.md | 230 | ## RAG integration | COMMENT |
| MEDIUM | backend/cli/skills/llm-tools/qdrant/SKILL.md | 265 | # RAG retrieval | COMMENT |
| MEDIUM | backend/cli/skills/llm-tools/qdrant/SKILL.md | 275 | # Use in RAG pipeline | COMMENT |
| MEDIUM | backend/cli/skills/llm-tools/whisper/SKILL.md | 244 | # Use transcription in RAG | COMMENT |
| MEDIUM | backend/cli/skills/chemistry/molfeat/SKILL.md | 154 | # MACCS - Fast, good for scaffold hopping | COMMENT |
| MEDIUM | backend/cli/skills/chemistry/molfeat/SKILL.md | 209 | # MACCS - Fast, scaffold-based similarity | COMMENT |
| MEDIUM | …/skills/chemistry/pytdc/scripts/load_and_split_data.py | 196 | # Example 1: Single prediction with scaffold split | COMMENT |
| MEDIUM⚡ | backend/cli/skills/chemistry/datamol/SKILL.md | 263 | # Get Bemis-Murcko scaffold (core structure) | COMMENT |
| MEDIUM⚡ | backend/cli/skills/chemistry/datamol/SKILL.md | 270 | # Group compounds by scaffold | COMMENT |
| MEDIUM⚡ | backend/cli/skills/chemistry/datamol/SKILL.md | 276 | # Count scaffold frequency | COMMENT |
| MEDIUM⚡ | backend/cli/skills/chemistry/datamol/SKILL.md | 280 | # Create scaffold-to-molecules mapping | COMMENT |
| MEDIUM | backend/cli/skills/chemistry/datamol/SKILL.md | 545 | # Group by scaffold | COMMENT |
| MEDIUM | backend/cli/skills/chemistry/datamol/SKILL.md | 556 | # Analyze each scaffold series | COMMENT |
| MEDIUM | …ls/chemistry/datamol/references/fragments_scaffolds.md | 3 | ## Scaffolds Module (`datamol.scaffold`) | COMMENT |
| MEDIUM⚡ | …ls/chemistry/datamol/references/fragments_scaffolds.md | 28 | # Count scaffold frequency | COMMENT |
| 33 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | …cli/skills/research/research-lookup/research_lookup.py | 358 | CODE | |
| LOW | …ls/research/research-lookup/scripts/research_lookup.py | 358 | CODE | |
| LOW | …scientific-schematics/scripts/generate_schematic_ai.py | 249 | CODE | |
| LOW | …scientific-schematics/scripts/generate_schematic_ai.py | 358 | CODE | |
| LOW | …scientific-schematics/scripts/generate_schematic_ai.py | 451 | CODE | |
| LOW | …visualization/protein-diagram/scripts/draw_features.py | 96 | CODE | |
| LOW | …sualization/protein-diagram/scripts/draw_domain_map.py | 34 | CODE | |
| LOW | …alization/protein-diagram/scripts/draw_ramachandran.py | 31 | CODE | |
| LOW | …zation/infographics/scripts/generate_infographic_ai.py | 398 | CODE | |
| LOW | …zation/infographics/scripts/generate_infographic_ai.py | 652 | CODE | |
| LOW | …zation/infographics/scripts/generate_infographic_ai.py | 813 | CODE | |
| LOW | …visualization/matplotlib/scripts/style_configurator.py | 196 | CODE | |
| LOW | …visualization/matplotlib/scripts/style_configurator.py | 277 | CODE | |
| LOW | …tion/scientific-visualization/scripts/style_presets.py | 111 | CODE | |
| LOW | …lls/llm-tools/generate-image/scripts/generate_image.py | 23 | CODE | |
| LOW | …lls/llm-tools/generate-image/scripts/generate_image.py | 87 | CODE | |
| LOW | …ills/databases/uspto-database/scripts/patent_search.py | 252 | CODE | |
| LOW | …s/databases/uspto-database/scripts/trademark_client.py | 226 | CODE | |
| LOW | …s/databases/uspto-database/scripts/trademark_client.py | 183 | CODE | |
| LOW | …skills/databases/uspto-database/scripts/peds_client.py | 214 | CODE | |
| LOW | …skills/databases/uspto-database/scripts/peds_client.py | 155 | CODE | |
| LOW | …s/databases/cosmic-database/scripts/download_cosmic.py | 30 | CODE | |
| LOW | …s/databases/gene-database/scripts/batch_gene_lookup.py | 96 | CODE | |
| LOW | …s/databases/gene-database/scripts/batch_gene_lookup.py | 182 | CODE | |
| LOW | …lls/databases/gene-database/scripts/fetch_gene_data.py | 157 | CODE | |
| LOW | …s/databases/biorxiv-database/scripts/biorxiv_search.py | 301 | CODE | |
| LOW | …atabases/pubchem-database/scripts/bioactivity_query.py | 255 | CODE | |
| LOW | …databases/drugbank-database/scripts/drugbank_helper.py | 277 | CODE | |
| LOW | …ases/brenda-database/scripts/enzyme_pathway_builder.py | 180 | CODE | |
| LOW | …ases/brenda-database/scripts/enzyme_pathway_builder.py | 274 | CODE | |
| LOW | …ases/brenda-database/scripts/enzyme_pathway_builder.py | 348 | CODE | |
| LOW | …ases/brenda-database/scripts/enzyme_pathway_builder.py | 450 | CODE | |
| LOW | …ases/brenda-database/scripts/enzyme_pathway_builder.py | 596 | CODE | |
| LOW | …ases/brenda-database/scripts/enzyme_pathway_builder.py | 696 | CODE | |
| LOW | …ases/brenda-database/scripts/enzyme_pathway_builder.py | 805 | CODE | |
| LOW | …ases/brenda-database/scripts/enzyme_pathway_builder.py | 463 | CODE | |
| LOW | …/skills/databases/fda-database/scripts/fda_examples.py | 144 | CODE | |
| LOW | …/skills/databases/fda-database/scripts/fda_examples.py | 252 | CODE | |
| LOW | …cli/skills/databases/fda-database/scripts/fda_query.py | 108 | CODE | |
| LOW | …ls/databases/ensembl-database/scripts/ensembl_query.py | 314 | CODE | |
| LOW | …ls/databases/ensembl-database/scripts/ensembl_query.py | 50 | CODE | |
| LOW | …ls/databases/clinpgx-database/scripts/query_clinpgx.py | 41 | CODE | |
| LOW | …s/databases/uniprot-database/scripts/uniprot_client.py | 233 | CODE | |
| LOW | …/databases/reactome-database/scripts/reactome_query.py | 241 | CODE | |
| LOW | …databases/openalex-database/scripts/openalex_client.py | 44 | CODE | |
| LOW | …databases/openalex-database/scripts/openalex_client.py | 238 | CODE | |
| LOW | …i/skills/chemistry/medchem/scripts/filter_molecules.py | 32 | CODE | |
| LOW | …i/skills/chemistry/medchem/scripts/filter_molecules.py | 114 | CODE | |
| LOW | …i/skills/chemistry/medchem/scripts/filter_molecules.py | 205 | CODE | |
| LOW | …/chemistry/molecular-docking/scripts/prepare_target.py | 104 | CODE | |
| LOW | …/chemistry/molecular-docking/scripts/prepare_target.py | 121 | CODE | |
| LOW | …/chemistry/molecular-docking/scripts/prepare_target.py | 162 | CODE | |
| LOW | …/chemistry/molecular-docking/scripts/prepare_target.py | 286 | CODE | |
| LOW | …/chemistry/molecular-docking/scripts/prepare_target.py | 355 | CODE | |
| LOW | …chemistry/molecular-docking/scripts/prepare_ligands.py | 47 | CODE | |
| LOW | …chemistry/molecular-docking/scripts/prepare_ligands.py | 155 | CODE | |
| LOW | …chemistry/molecular-docking/scripts/prepare_ligands.py | 186 | CODE | |
| LOW | …chemistry/molecular-docking/scripts/prepare_ligands.py | 255 | CODE | |
| LOW | …cli/skills/chemistry/molecular-docking/scripts/dock.py | 159 | CODE | |
| LOW | …cli/skills/chemistry/molecular-docking/scripts/dock.py | 242 | CODE | |
| 224 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| HIGH | …nd/cli/test/skill/image-generation-entrypoints.test.ts | 49 | print(json.dumps({ | CODE |
| HIGH | …nd/cli/test/skill/image-generation-entrypoints.test.ts | 91 | print(json.dumps(errors)) | CODE |
| HIGH | backend/cli/src/file/science.ts | 51 | print(json.dumps({"error": "h5py is not available", "detail": str(exc)})) | CODE |
| HIGH | backend/cli/src/file/science.ts | 172 | print(json.dumps(result)) | CODE |
| HIGH | backend/cli/src/cli/ui.ts | 61 | print(...message) | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 298 | return False | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 304 | return False | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 306 | return True | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 344 | return False | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 347 | return False | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 348 | return True | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 693 | return None | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 698 | return False | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 708 | return False | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 711 | return False | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 748 | return True | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 750 | return False | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 752 | return False | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 759 | return False | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 767 | return True | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 905 | elif value["scheduler"] == "pbs": | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 1151 | elif action == "submit": submit(token) | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 1152 | elif action == "status": status(token, sys.argv[3]) | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 1153 | elif action == "cancel": cancel(token, sys.argv[3]) | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 1154 | elif action == "log": logs(token, sys.argv[3]) | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 1155 | elif action == "harvest": harvest(token) | CODE |
| HIGH⚡ | backend/cli/src/compute/ssh/adapter.ts | 1156 | elif action == "release": release(token) | CODE |
| HIGH | backend/cli/src/compute/ssh/adapter.ts | 214 | return None | CODE |
| HIGH | backend/cli/src/compute/ssh/adapter.ts | 245 | return None | CODE |
| HIGH | backend/cli/src/compute/ssh/adapter.ts | 460 | return False | CODE |
| HIGH | backend/cli/src/compute/ssh/adapter.ts | 462 | return True | CODE |
| HIGH | backend/cli/src/compute/ssh/adapter.ts | 1021 | elif identifier.startswith("pbs:"): | CODE |
| HIGH | backend/cli/src/compute/ssh/adapter.ts | 1041 | elif not scope_empty(value): | CODE |
| HIGH | backend/cli/src/compute/ssh/adapter.ts | 1218 | print(json.dumps({"staged": True, "files": len(manifest["files"])})) | CODE |
| HIGH | backend/cli/src/tool/biology/notebook.ts | 77 | print(repr(result)) | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | …esearch/perplexity-search/scripts/perplexity_search.py | 23 | CODE | |
| LOW | …esearch/perplexity-search/scripts/perplexity_search.py | 29 | CODE | |
| LOW | …alization/protein-diagram/scripts/draw_ramachandran.py | 28 | CODE | |
| LOW | …tion/dna-visualization/scripts/draw_restriction_map.py | 28 | CODE | |
| LOW | …tion/dna-visualization/scripts/draw_restriction_map.py | 29 | CODE | |
| LOW | …tion/dna-visualization/scripts/draw_restriction_map.py | 19 | CODE | |
| LOW | …visualization/matplotlib/scripts/style_configurator.py | 20 | CODE | |
| LOW | …ills/visualization/matplotlib/scripts/plot_template.py | 286 | CODE | |
| LOW | …tion/scientific-visualization/scripts/figure_export.py | 11 | CODE | |
| LOW | …tion/scientific-visualization/scripts/style_presets.py | 11 | CODE | |
| LOW | …ugging-face-tool-builder/references/baseline_hf_api.py | 9 | CODE | |
| LOW | …ills/databases/uspto-database/scripts/patent_search.py | 20 | CODE | |
| LOW | …ills/databases/uspto-database/scripts/patent_search.py | 21 | CODE | |
| LOW | …i/skills/databases/gene-database/scripts/query_gene.py | 16 | CODE | |
| LOW | …s/databases/biorxiv-database/scripts/biorxiv_search.py | 14 | CODE | |
| LOW | …s/databases/biorxiv-database/scripts/biorxiv_search.py | 17 | CODE | |
| LOW | …/databases/fred-economic-data/scripts/fred_examples.py | 9 | CODE | |
| LOW | …lls/databases/fred-economic-data/scripts/fred_query.py | 11 | CODE | |
| LOW | …databases/drugbank-database/scripts/drugbank_helper.py | 20 | CODE | |
| LOW | …abases/brenda-database/scripts/brenda_visualization.py | 26 | CODE | |
| LOW | …abases/brenda-database/scripts/brenda_visualization.py | 28 | CODE | |
| LOW | …abases/brenda-database/scripts/brenda_visualization.py | 28 | CODE | |
| LOW | …abases/brenda-database/scripts/brenda_visualization.py | 41 | CODE | |
| LOW | …abases/brenda-database/scripts/brenda_visualization.py | 41 | CODE | |
| LOW | …abases/brenda-database/scripts/brenda_visualization.py | 41 | CODE | |
| LOW | …abases/brenda-database/scripts/brenda_visualization.py | 41 | CODE | |
| LOW | …abases/brenda-database/scripts/brenda_visualization.py | 41 | CODE | |
| LOW | …ases/brenda-database/scripts/enzyme_pathway_builder.py | 27 | CODE | |
| LOW | …ases/brenda-database/scripts/enzyme_pathway_builder.py | 29 | CODE | |
| LOW | …ases/brenda-database/scripts/enzyme_pathway_builder.py | 29 | CODE | |
| LOW | …ases/brenda-database/scripts/enzyme_pathway_builder.py | 29 | CODE | |
| LOW | …ases/brenda-database/scripts/enzyme_pathway_builder.py | 30 | CODE | |
| LOW | …ases/brenda-database/scripts/enzyme_pathway_builder.py | 40 | CODE | |
| LOW | …ases/brenda-database/scripts/enzyme_pathway_builder.py | 54 | CODE | |
| LOW | …cli/skills/databases/fda-database/scripts/fda_query.py | 21 | CODE | |
| LOW | …cli/skills/databases/fda-database/scripts/fda_query.py | 22 | CODE | |
| LOW | …skills/databases/string-database/scripts/string_api.py | 17 | CODE | |
| LOW | …skills/databases/string-database/scripts/string_api.py | 18 | CODE | |
| LOW | …skills/databases/string-database/scripts/string_api.py | 18 | CODE | |
| LOW | …s/databases/uniprot-database/scripts/uniprot_client.py | 29 | CODE | |
| LOW | …/databases/reactome-database/scripts/reactome_query.py | 25 | CODE | |
| LOW | …linicaltrials-database/scripts/query_clinicaltrials.py | 16 | CODE | |
| LOW | …i/skills/chemistry/medchem/scripts/filter_molecules.py | 17 | CODE | |
| LOW | …i/skills/chemistry/medchem/scripts/filter_molecules.py | 18 | CODE | |
| LOW | …/chemistry/molecular-docking/scripts/prepare_target.py | 52 | CODE | |
| LOW | …chemistry/molecular-docking/scripts/prepare_ligands.py | 29 | CODE | |
| LOW | …chemistry/molecular-docking/scripts/prepare_ligands.py | 37 | CODE | |
| LOW | …cli/skills/chemistry/molecular-docking/scripts/dock.py | 22 | CODE | |
| LOW | …cli/skills/chemistry/molecular-docking/scripts/dock.py | 53 | CODE | |
| LOW | …li/skills/chemistry/molecular-docking/scripts/score.py | 17 | CODE | |
| LOW | …li/skills/chemistry/molecular-docking/scripts/score.py | 31 | CODE | |
| LOW | …li/skills/chemistry/molecular-docking/scripts/score.py | 31 | CODE | |
| LOW | …li/skills/chemistry/molecular-docking/scripts/score.py | 31 | CODE | |
| LOW | …li/skills/chemistry/molecular-docking/scripts/score.py | 32 | CODE | |
| LOW | …li/skills/chemistry/molecular-docking/scripts/score.py | 52 | CODE | |
| LOW | …li/skills/chemistry/molecular-docking/scripts/score.py | 52 | CODE | |
| LOW | …li/skills/chemistry/molecular-docking/scripts/score.py | 53 | CODE | |
| LOW | …lls/chemistry/structure-prediction/scripts/evaluate.py | 31 | CODE | |
| LOW | …ills/chemistry/structure-prediction/scripts/compare.py | 14 | CODE | |
| LOW | …ills/chemistry/structure-prediction/scripts/compare.py | 19 | CODE | |
| 121 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| HIGH | …cli/skills/databases/kegg-database/scripts/kegg_api.py | 44 | List entry identifiers and associated names. Args: database: KEGG database name or specific entry (e.g | STRING |
| HIGH | …cli/skills/databases/kegg-database/scripts/kegg_api.py | 72 | Search for entries by keywords or molecular properties. Args: database: Database to search ('genes', ' | STRING |
| HIGH | …cli/skills/databases/kegg-database/scripts/kegg_api.py | 111 | Retrieve full database entries or specific data formats. Args: entries: Single entry ID or list of ent | STRING |
| HIGH | …cli/skills/databases/kegg-database/scripts/kegg_api.py | 158 | Convert identifiers between KEGG and external databases. Args: target_db: Target database (e.g., 'ncbi | STRING |
| HIGH | …cli/skills/databases/kegg-database/scripts/kegg_api.py | 187 | Find related entries across KEGG databases. Args: target_db: Target database (e.g., 'pathway', 'enzyme | STRING |
| HIGH | …ls/databases/ensembl-database/scripts/ensembl_query.py | 58 | Make an API request with error handling and retries. Args: endpoint: API endpoint path | STRING |
| HIGH | …skills/databases/string-database/scripts/string_api.py | 29 | Map protein names, synonyms, and identifiers to STRING IDs. Args: identifiers: Single protein identifi | STRING |
| HIGH | …skills/databases/string-database/scripts/string_api.py | 78 | Get protein-protein interaction network data. Args: identifiers: Protein identifier(s) - use STRING ID | STRING |
| HIGH | …ases/opentargets-database/scripts/query_opentargets.py | 22 | Execute a GraphQL query against the Open Targets Platform API. Args: query: GraphQL query string | STRING |
| HIGH | …gineering/hugging-face-datasets/scripts/sql_manager.py | 134 | Execute SQL query on a Hugging Face dataset. Args: dataset_id: Dataset ID (e.g., "cais/mml | STRING |
| HIGH | …gineering/hugging-face-datasets/scripts/sql_manager.py | 356 | Filter and transform dataset with SQL clauses. Args: dataset_id: Dataset ID se | STRING |
| HIGH | …d/cli/skills/ml-training/adaptyv/reference/examples.md | 505 | Request a custom antigen not in the standard catalog Args: target_name: Name of the target protein | STRING |
| HIGH | …d/cli/skills/ml-training/adaptyv/reference/examples.md | 758 | Make API request with retry logic and error handling Args: method: HTTP method (GET, POST, etc.) | STRING |
| HIGH | …kills/biology/clinical-imaging/scripts/hemodynamics.py | 37 | Load blood pressure waveform data from CSV. Accepts CSV with columns 'time' and 'pressure', or just 'pressure' | STRING |
| HIGH | …kills/biology/clinical-imaging/scripts/ciliary_beat.py | 39 | Load video frames as grayscale numpy array. Args: video_path: Path to video file. fps_override | STRING |
| HIGH | …skills/biology/clinical-imaging/scripts/compute_adc.py | 46 | Load diffusion-weighted NIfTI image. Args: dwi_path: Path to 4D NIfTI DWI file. Returns: | STRING |
| HIGH | …skills/biology/clinical-imaging/scripts/compute_adc.py | 75 | Load binary brain mask NIfTI image. Args: mask_path: Path to 3D NIfTI mask file. Returns: | STRING |
| HIGH | …skills/biology/clinical-imaging/scripts/compute_adc.py | 104 | Parse comma-separated b-value string into sorted numpy array. Args: bvalues_str: Comma-separated b-val | STRING |
| HIGH | …ls/biology/clinical-imaging/scripts/amyloid_plaques.py | 46 | Load microscopy image from file. Args: image_path: Path to image file (TIFF, PNG, JPEG, etc.). Re | STRING |
| HIGH | …ls/biology/clinical-imaging/scripts/amyloid_plaques.py | 105 | Threshold grayscale image to produce binary mask. Args: gray: 2D uint8 grayscale image (already smooth | STRING |
| HIGH | …s/biology/clinical-imaging/scripts/cosinor_analysis.py | 41 | Load time-series data from CSV. Expected columns: 'time' (hours) and 'value' (measurement). Args: | STRING |
| HIGH | …s/biology/clinical-imaging/scripts/cosinor_analysis.py | 99 | Fit cosinor model to data using least-squares optimization. Args: time: 1D array of time points (hours | STRING |
| HIGH | …ls/biology/bioimage-analysis/scripts/colocalization.py | 38 | Load a single fluorescence channel image as a 2D grayscale array. Args: image_path: Path to the channel ima | STRING |
| HIGH | …ls/biology/bioimage-analysis/scripts/colocalization.py | 82 | Apply a thresholding method to create a binary mask of signal pixels. Args: image: 2D float array of channe | STRING |
| HIGH | …ls/biology/bioimage-analysis/scripts/count_colonies.py | 39 | Load an image from disk using OpenCV. Args: image_path: Path to the image file. Returns: numpy | STRING |
| HIGH | …iology/bioimage-analysis/scripts/analyze_morphology.py | 39 | Load a microscopy image from file. Args: image_path: Path to the image file. Returns: numpy.nd | STRING |
| HIGH | …iology/bioimage-analysis/scripts/analyze_morphology.py | 75 | Load a pre-segmented integer label mask. Args: mask_path: Path to the mask image file. Returns: | STRING |
| HIGH | …kills/biology/bioimage-analysis/scripts/track_cells.py | 39 | Load time-lapse frames from a directory of images or a multi-frame TIFF. Args: image_source: Path to a dire | STRING |
| HIGH | …lls/biology/bioimage-analysis/scripts/segment_cells.py | 38 | Load a microscopy image from file. Supports TIFF (via tifffile), PNG, JPEG, and other formats via skimage. Arg | STRING |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | backend/cli/test/agent/harness-contract.test.ts | 210 | expect(skill).not.toContain("### Step 5: Save Report") | CODE |
| LOW | …s/databases/cosmic-database/scripts/download_cosmic.py | 64 | # Step 1: Get the download URL | COMMENT |
| LOW⚡ | …s/databases/cosmic-database/scripts/download_cosmic.py | 91 | # Step 2: Download the file | COMMENT |
| LOW⚡ | …s/databases/cosmic-database/scripts/download_cosmic.py | 99 | # Step 3: Write to disk | COMMENT |
| LOW⚡ | …atabases/pubchem-database/scripts/bioactivity_query.py | 307 | # Step 1: Find assays for the target | COMMENT |
| LOW⚡ | …atabases/pubchem-database/scripts/bioactivity_query.py | 314 | # Step 2: Get active compounds from these assays | COMMENT |
| LOW | …s/databases/uniprot-database/scripts/uniprot_client.py | 164 | # Step 1: Submit job | COMMENT |
| LOW | …s/databases/uniprot-database/scripts/uniprot_client.py | 177 | # Step 2: Poll for completion | COMMENT |
| LOW | …s/databases/uniprot-database/scripts/uniprot_client.py | 190 | # Step 3: Retrieve results | COMMENT |
| LOW | …s/databases/openalex-database/scripts/query_helpers.py | 28 | # Step 1: Find author ID | COMMENT |
| LOW | …s/databases/openalex-database/scripts/query_helpers.py | 43 | # Step 2: Get works by author | COMMENT |
| LOW | …s/databases/openalex-database/scripts/query_helpers.py | 74 | # Step 1: Find institution ID | COMMENT |
| LOW | …s/databases/openalex-database/scripts/query_helpers.py | 89 | # Step 2: Get works from institution | COMMENT |
| LOW | …s/databases/openalex-database/scripts/query_helpers.py | 234 | # Step 1: Find entity | COMMENT |
| LOW | …s/databases/openalex-database/scripts/query_helpers.py | 246 | # Step 2: Get statistics | COMMENT |
| LOW⚡ | …skills/coding/pymoo/scripts/decision_making_example.py | 138 | # Step 1: Run optimization | COMMENT |
| LOW⚡ | …skills/coding/pymoo/scripts/decision_making_example.py | 141 | # Step 2: Find extreme solutions | COMMENT |
| LOW⚡ | …skills/coding/pymoo/scripts/decision_making_example.py | 144 | # Step 3: Compare different preference weights | COMMENT |
| LOW⚡ | …skills/coding/pymoo/scripts/decision_making_example.py | 147 | # Step 4: Visualize selections with petal diagram | COMMENT |
| LOW⚡ | …/hugging-face-model-trainer/scripts/convert_to_gguf.py | 158 | # Step 2: Save merged model temporarily | COMMENT |
| LOW⚡ | …/hugging-face-model-trainer/scripts/convert_to_gguf.py | 169 | # Step 3: Install llama.cpp for conversion | COMMENT |
| LOW⚡ | …/hugging-face-model-trainer/scripts/convert_to_gguf.py | 281 | # Step 6: Upload to Hub | COMMENT |
| LOW | …/hugging-face-model-trainer/scripts/convert_to_gguf.py | 121 | # Step 1: Load base model and adapter | COMMENT |
| LOW | …/hugging-face-model-trainer/scripts/convert_to_gguf.py | 199 | # Step 4: Convert to GGUF (FP16) | COMMENT |
| LOW | …/hugging-face-model-trainer/scripts/convert_to_gguf.py | 223 | # Step 5: Quantize to different formats | COMMENT |
| LOW⚡ | …ls/biology/synthetic-biology/scripts/codon_optimize.py | 447 | # Step 1: Replace with optimal codons | COMMENT |
| LOW⚡ | …ls/biology/synthetic-biology/scripts/codon_optimize.py | 457 | # Step 2: Remove restriction sites | COMMENT |
| LOW⚡ | …ls/biology/synthetic-biology/scripts/codon_optimize.py | 460 | # Step 3: Fix GC content | COMMENT |
| LOW⚡ | …ls/biology/synthetic-biology/scripts/codon_optimize.py | 463 | # Step 4: Remove homopolymer runs | COMMENT |
| LOW⚡ | …skills/biology/deeptools/scripts/workflow_generator.py | 72 | # Step 2: Coverage assessment | COMMENT |
| LOW⚡ | …skills/biology/deeptools/scripts/workflow_generator.py | 80 | # Step 3: Fragment size (for paired-end data) | COMMENT |
| LOW⚡ | …skills/biology/deeptools/scripts/workflow_generator.py | 87 | # Step 4: ChIP signal strength | COMMENT |
| LOW⚡ | …skills/biology/deeptools/scripts/workflow_generator.py | 307 | # Step 2: Generate coverage track | COMMENT |
| LOW⚡ | …skills/biology/deeptools/scripts/workflow_generator.py | 317 | # Step 3: Fragment size analysis | COMMENT |
| LOW⚡ | …skills/biology/deeptools/scripts/workflow_generator.py | 324 | # Step 4: Compute matrix at peaks (if peaks provided) | COMMENT |
| LOW | …skills/biology/deeptools/scripts/workflow_generator.py | 51 | # Step 1: Correlation analysis | COMMENT |
| LOW | …skills/biology/deeptools/scripts/workflow_generator.py | 128 | # Step 1: Generate normalized coverage tracks | COMMENT |
| LOW | …skills/biology/deeptools/scripts/workflow_generator.py | 151 | # Step 2: Create log2 ratio track | COMMENT |
| LOW | …skills/biology/deeptools/scripts/workflow_generator.py | 164 | # Step 3: Compute matrix around TSS | COMMENT |
| LOW | …skills/biology/deeptools/scripts/workflow_generator.py | 178 | # Step 4: Generate heatmap | COMMENT |
| LOW | …skills/biology/deeptools/scripts/workflow_generator.py | 191 | # Step 5: Generate profile plot | COMMENT |
| LOW | …skills/biology/deeptools/scripts/workflow_generator.py | 203 | # Step 6: Enrichment at peaks (if peaks provided) | COMMENT |
| LOW | …skills/biology/deeptools/scripts/workflow_generator.py | 294 | # Step 1: Shift reads for Tn5 correction | COMMENT |
| LOW⚡ | …gy/opentrons-integration/scripts/pcr_setup_template.py | 80 | # Step 1: Distribute master mix | COMMENT |
| LOW⚡ | …gy/opentrons-integration/scripts/pcr_setup_template.py | 90 | # Step 2: Add template DNA | COMMENT |
| LOW⚡ | …ntrons-integration/scripts/serial_dilution_template.py | 65 | # Step 1: Add diluent to all wells except first column | COMMENT |
| LOW⚡ | …ntrons-integration/scripts/serial_dilution_template.py | 75 | # Step 2: Add stock solution to first column | COMMENT |
| LOW⚡ | …ntrons-integration/scripts/serial_dilution_template.py | 84 | # Step 3: Perform serial dilution | COMMENT |
| LOW⚡ | …iology/bioservices/scripts/compound_cross_reference.py | 337 | # Step 1: Search KEGG | STRING |
| LOW⚡ | …iology/bioservices/scripts/compound_cross_reference.py | 343 | # Step 2: Get KEGG details | STRING |
| LOW⚡ | …iology/bioservices/scripts/compound_cross_reference.py | 346 | # Step 3: Map to ChEMBL | STRING |
| LOW⚡ | …iology/bioservices/scripts/compound_cross_reference.py | 349 | # Step 4: Get ChEBI details | STRING |
| LOW⚡ | …iology/bioservices/scripts/compound_cross_reference.py | 354 | # Step 5: Get ChEMBL details | STRING |
| LOW⚡ | …ology/bioservices/scripts/protein_analysis_workflow.py | 368 | # Step 1: Search protein | STRING |
| LOW⚡ | …ology/bioservices/scripts/protein_analysis_workflow.py | 374 | # Step 2: Retrieve sequence | STRING |
| LOW⚡ | …ology/bioservices/scripts/protein_analysis_workflow.py | 379 | # Step 3: BLAST search | STRING |
| LOW⚡ | …ology/bioservices/scripts/protein_analysis_workflow.py | 383 | # Step 4: Pathway discovery | STRING |
| LOW⚡ | …ology/bioservices/scripts/protein_analysis_workflow.py | 387 | # Step 5: Interaction mapping | STRING |
| LOW⚡ | …ology/bioservices/scripts/protein_analysis_workflow.py | 390 | # Step 6: GO annotations | STRING |
| LOW | …skills/biology/gget/scripts/batch_sequence_analysis.py | 67 | # Step 1: BLAST each sequence | COMMENT |
| 13 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| CRITICAL | evals/launch/capture.ts | 501 | `observable=${result.result.completion.observableComplete ? "complete" : "incomplete"} · ${result.result.observabl | CODE |
| CRITICAL | evals/cadence-harness/run.ts | 287 | jobs = await unwrap<Json[]>(input.client.settings.compute.jobs.list()) | CODE |
| CRITICAL | frontend/landing/public/docs/assets/index-Cazmh0hf.js | 731 | `,h="/",b="*",y="",S="comment",x="declaration";function T(Z,D){if(typeof Z!="string")throw new TypeError("First argument | CODE |
| CRITICAL | frontend/landing/public/docs/assets/index-Cazmh0hf.js | 758 | `))}function m(x,T,U,Z){const D=U.enter("tableCell"),F=U.enter("phrasing"),Q=U.containerPhrasing(x,{...Z,before:d,after: | CODE |
| CRITICAL⚡ | …e/src/science/renderers/molecular/ProteinStructure.tsx | 94 | subscriptions.push(p.managers.structure.selection.events.changed.subscribe(syncSelection)) | CODE |
| CRITICAL⚡ | …e/src/science/renderers/molecular/ProteinStructure.tsx | 95 | subscriptions.push(p.managers.structure.selection.events.additionsHistoryUpdated.subscribe(syncSelection)) | CODE |
| CRITICAL⚡ | …e/src/science/renderers/molecular/ProteinStructure.tsx | 96 | subscriptions.push(p.managers.structure.measurement.behaviors.state.subscribe(syncMeasurements)) | CODE |
| CRITICAL | …ckend/cli/skills/ml-training/axolotl/references/api.md | 658 | core.trainers.grpo.sampler.SequenceParallelRepeatRandomSampler.set_epoch(epoch) | CODE |
| CRITICAL | …ckend/cli/skills/ml-training/axolotl/references/api.md | 1795 | core.trainers.grpo.trainer.AxolotlGRPOSequenceParallelTrainer.get_train_dataloader( | CODE |
| CRITICAL | …ckend/cli/skills/ml-training/axolotl/references/api.md | 4690 | core.trainers.dpo.trainer.AxolotlDPOTrainer.push_to_hub(*args, **kwargs) | CODE |
| CRITICAL | …ckend/cli/skills/ml-training/axolotl/references/api.md | 4892 | core.trainers.mixins.scheduler.SchedulerMixin.create_scheduler( | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | frontend/ui/src/context/marked.tsx | 41 | // "gitDecoration.untrackedResourceForeground": "#00cab1", | COMMENT |
| LOW | frontend/ui/src/pierre/index.ts | 161 | // numCol.dataset["slot"] = "diff-hunk-separator-line-number" | COMMENT |
| LOW | frontend/workspace/src/components/terminal-error.ts | 1 | // When a pty socket dies, WebKit dispatches a bare `error` Event (no detail) | COMMENT |
| LOW | frontend/workspace/src/components/settings/registry.ts | 1 | import { lazy, type Component } from "solid-js" | COMMENT |
| LOW | frontend/workspace/src/atlas/poll-identity.ts | 1 | // A polling surface has to name itself to the server. Both compute samplers | COMMENT |
| LOW | frontend/workspace/src/atlas/FileExplorer.test.ts | 1 | import { describe, expect, test } from "bun:test" | COMMENT |
| LOW | backend/cli/bunfig.toml | 1 | [test] | COMMENT |
| LOW | backend/cli/parsers-config.ts | 141 | // NOTE: This nvim-treesitter query is currently broken, because the parser is not compatible with the query a | COMMENT |
| LOW | backend/cli/test/preload.ts | 61 | COMMENT | |
| LOW | backend/cli/test/auth/billing-flip.test.ts | 1 | import { test, expect, afterEach } from "bun:test" | COMMENT |
| LOW | backend/cli/test/science/kernel/metrics.test.ts | 461 | COMMENT | |
| LOW | backend/cli/test/science/kernel/metrics.test.ts | 801 | // The grandchild alone holds 64MB the leader never touches, so the | COMMENT |
| LOW | backend/cli/test/provider/managed-routing.test.ts | 721 | // google-vertex autoloads off GOOGLE_CLOUD_PROJECT alone (no auth.json | COMMENT |
| LOW | backend/cli/test/tool/question.test.ts | 61 | askSpy.mockResolvedValueOnce([["Dog"]]) | COMMENT |
| LOW | backend/cli/test/tool/question.test.ts | 81 | // } catch (e: any) { | COMMENT |
| LOW | backend/cli/test/tool/question.test.ts | 101 | // expect(true).toBe(false) | COMMENT |
| LOW | …conducting-scientific-research/references/templates.md | 1 | # Project record templates | COMMENT |
| LOW | …d/cli/skills/llm-tools/outlines/references/backends.md | 221 | # - Speed: Slightly slower than Q4 | COMMENT |
| LOW | …databases/drugbank-database/references/drug-queries.md | 181 | # Common properties to extract: | COMMENT |
| LOW | …chemistry/diffdock/assets/custom_inference_config.yaml | 41 | COMMENT | |
| LOW | …chemistry/diffdock/assets/custom_inference_config.yaml | 61 | # temp_sampling_tor: 6.5 | COMMENT |
| LOW | …chemistry/diffdock/assets/custom_inference_config.yaml | 81 | # temp_sampling_rot: 2.0 | COMMENT |
| LOW | …skills/ml-inference/vllm/references/troubleshooting.md | 441 | COMMENT | |
| LOW | …skills/ml-inference/tensorrt-llm/references/serving.md | 161 | curl http://localhost:9090/metrics | COMMENT |
| LOW | …/other/hugging-face-jobs/scripts/generate-responses.py | 1 | # /// script | COMMENT |
| LOW | …s/other/hugging-face-jobs/scripts/cot-self-instruct.py | 1 | # /// script | COMMENT |
| LOW | …cloud-compute/lambda-labs/references/advanced-usage.md | 281 | ### Slurm job submission | COMMENT |
| LOW | backend/cli/skills/data-engineering/markitdown/SKILL.md | 181 | COMMENT | |
| LOW | …d/cli/skills/coding/exploratory-data-analysis/SKILL.md | 301 | COMMENT | |
| LOW | …ckend/cli/skills/coding/denario/references/examples.md | 41 | ### Execute Full Pipeline | COMMENT |
| LOW | …ckend/cli/skills/coding/denario/references/examples.md | 61 | # - Computed trend: +0.18°C per decade | COMMENT |
| LOW | …ckend/cli/skills/coding/denario/references/examples.md | 81 | # climate_research/ | COMMENT |
| LOW | …ckend/cli/skills/coding/denario/references/examples.md | 421 | # - ROC curves | COMMENT |
| LOW | …ysics/pymatgen/references/transformations_workflows.md | 301 | relax = MPRelaxSet(slab) | COMMENT |
| LOW | backend/cli/skills/ml-training/moe-training/SKILL.md | 401 | COMMENT | |
| LOW | …training/accelerate/references/megatron-integration.md | 421 | # checkpoint-1000/ | COMMENT |
| LOW | …cli/skills/ml-training/knowledge-distillation/SKILL.md | 221 | COMMENT | |
| LOW | backend/cli/skills/ml-training/rwkv/SKILL.md | 141 | COMMENT | |
| LOW | backend/cli/skills/ml-training/model-pruning/SKILL.md | 241 | - 50% sparsity (2:4) → 2× speedup on NVIDIA GPUs | COMMENT |
| LOW | …g/prime-intellect-lab/templates/basic_rl_training.toml | 1 | # Prime Intellect Lab — RL Training Configuration | COMMENT |
| LOW | …g/prime-intellect-lab/templates/basic_rl_training.toml | 21 | # "Qwen/Qwen3-235B-Instruct-2507" — Frontier-level (MoE) | COMMENT |
| LOW | …g/prime-intellect-lab/templates/basic_rl_training.toml | 41 | # LARGE RUN — Full training (~8-24 hours) | COMMENT |
| LOW | …g/prime-intellect-lab/templates/basic_rl_training.toml | 61 | id = "primeintellect/alphabet-sort" # Environment ID (owner/name) | COMMENT |
| LOW | …/skills/ml-training/gptq/references/troubleshooting.md | 61 | # Requantize with better calibration | COMMENT |
| LOW | …l-training/stable-baselines3/scripts/evaluate_agent.py | 201 | # Example 1: Evaluate a trained model | COMMENT |
| LOW | …l-training/stable-baselines3/scripts/evaluate_agent.py | 221 | # watch_agent( | COMMENT |
| LOW | …l-training/stable-baselines3/scripts/evaluate_agent.py | 241 | # model_path="./models/best_model/best_model.zip", | COMMENT |
| LOW | …l-training/stable-baselines3/scripts/train_rl_agent.py | 141 | algorithm=PPO, | COMMENT |
| LOW | …l-training/stable-baselines3/scripts/train_rl_agent.py | 161 | # algorithm=DQN, | COMMENT |
| LOW | …ining/stable-baselines3/scripts/custom_env_template.py | 61 | # 2. Multi-discrete: spaces.MultiDiscrete([n1, n2, ...]) | COMMENT |
| LOW | …gging-face-model-trainer/references/gguf_conversion.md | 61 | ### 3. ✅ Include All Dependencies | COMMENT |
| LOW | …ace-model-trainer/references/reliability_principles.md | 161 | # /// | COMMENT |
| LOW | …/hugging-face-model-trainer/scripts/convert_to_gguf.py | 1 | #!/usr/bin/env python3 | COMMENT |
| LOW | …ugging-face-model-trainer/scripts/train_sft_example.py | 1 | #!/usr/bin/env python3 | COMMENT |
| LOW | …end/cli/skills/ml-training/axolotl/references/other.md | 1841 | # The name of the chat template to use for training, following values are supported: | COMMENT |
| LOW | …end/cli/skills/ml-training/axolotl/references/other.md | 1881 | # message_property_mappings={'role':'role', 'content':'content'}) If a property exists | COMMENT |
| LOW | …end/cli/skills/ml-training/axolotl/references/other.md | 1901 | # Roles to train on. The tokens from these roles will be considered for the loss. | COMMENT |
| LOW | …end/cli/skills/ml-training/axolotl/references/other.md | 2001 | # will raise an error. This is the default. | COMMENT |
| LOW | …end/cli/skills/ml-training/axolotl/references/other.md | 2041 | # 'from' is loaded from input dataset and used as 'role', while 'value' is loaded and | COMMENT |
| LOW | …end/cli/skills/ml-training/axolotl/references/other.md | 2061 | # all EOS tokens, turn (default): train on the EOS token at the end of each trainable | COMMENT |
| 70 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | …esearch/perplexity-search/scripts/perplexity_search.py | 120 | # Check if citations are available in the response | COMMENT |
| LOW | …cli/skills/research/research-lookup/research_lookup.py | 432 | # Display results in human-readable format | COMMENT |
| LOW | …ls/research/research-lookup/scripts/research_lookup.py | 432 | # Display results in human-readable format | COMMENT |
| LOW | …scientific-schematics/scripts/generate_schematic_ai.py | 712 | # Check if quality is acceptable - STOP EARLY if so | COMMENT |
| LOW | …zation/infographics/scripts/generate_infographic_ai.py | 1149 | # Check if quality is acceptable | STRING |
| LOW | …g-face-tool-builder/references/find_models_by_paper.sh | 93 | # Check if the input looks like an arXiv ID (format: YYYY.NNNNN or YYYY.NNNNNNN) | COMMENT |
| LOW | …g-face-tool-builder/references/find_models_by_paper.sh | 133 | # Check if we got a valid response | COMMENT |
| LOW⚡ | …ills/databases/uspto-database/scripts/patent_search.py | 281 | # Print results | COMMENT |
| LOW⚡ | …s/databases/gene-database/scripts/batch_gene_lookup.py | 281 | # Output results | STRING |
| LOW | …s/databases/biorxiv-database/scripts/biorxiv_search.py | 224 | # Check if any keyword matches | COMMENT |
| LOW | …s/databases/biorxiv-database/scripts/biorxiv_search.py | 418 | # Output results | COMMENT |
| LOW⚡ | …ls/databases/brenda-database/scripts/brenda_queries.py | 220 | # Check if our target product is in the products list | COMMENT |
| LOW | …ls/databases/brenda-database/scripts/brenda_queries.py | 590 | # Check if organism might be thermophilic based on name | COMMENT |
| LOW⚡ | …ases/brenda-database/scripts/enzyme_pathway_builder.py | 287 | # Check if substrate is in the reactants | COMMENT |
| LOW⚡ | …ases/brenda-database/scripts/enzyme_pathway_builder.py | 302 | # Check if product is mentioned in substrate data (limited approach) | COMMENT |
| LOW | …ases/brenda-database/scripts/enzyme_pathway_builder.py | 184 | # Check if it's in the database | COMMENT |
| LOW | …ases/brenda-database/scripts/enzyme_pathway_builder.py | 380 | # Check if current metabolite is a starting material | COMMENT |
| LOW | …cli/skills/databases/fda-database/scripts/fda_query.py | 40 | # Check if at limit | COMMENT |
| LOW | …databases/openalex-database/scripts/openalex_client.py | 222 | # Check if we've hit max_results | COMMENT |
| LOW | …databases/openalex-database/scripts/openalex_client.py | 226 | # Check if there are more pages | COMMENT |
| LOW | …linicaltrials-database/scripts/query_clinicaltrials.py | 158 | # Check if we've reached the max or there are no more results | COMMENT |
| LOW | …chemistry/molecular-docking/scripts/prepare_ligands.py | 162 | # Check if input is a file | COMMENT |
| LOW⚡ | …cli/skills/chemistry/molecular-docking/scripts/dock.py | 61 | # Check if DiffDock CLI is available | COMMENT |
| LOW | …ls/chemistry/admet-prediction/scripts/compare_drugs.py | 523 | # Print results | STRING |
| LOW | …i/skills/chemistry/diffdock/scripts/analyze_results.py | 36 | # Check if this is a single complex or batch results | COMMENT |
| LOW | …skills/chemistry/diffdock/scripts/prepare_batch_csv.py | 130 | # Check if it's a file path or SMILES | COMMENT |
| LOW⚡ | …skills/chemistry/binding-affinity/scripts/consensus.py | 132 | # Check if it's rescore or interactions | COMMENT |
| LOW | …kills/chemistry/deepchem/scripts/predict_solubility.py | 150 | # Display results | COMMENT |
| LOW | …kills/chemistry/denovo-design/scripts/generate_sbdd.py | 205 | # Check if this residue matches any specified | COMMENT |
| LOW | …li/skills/chemistry/rdkit/scripts/similarity_search.py | 288 | # Output results | STRING |
| LOW | …skills/chemistry/rdkit/scripts/molecular_properties.py | 131 | # Output results | COMMENT |
| LOW | …li/skills/chemistry/pocket-detection/scripts/detect.py | 735 | # Print results | STRING |
| LOW | …er/get-available-resources/scripts/detect_resources.py | 155 | # Check if running on Apple Silicon | COMMENT |
| LOW | …/other/iso-13485-certification/scripts/gap_analyzer.py | 208 | # Read file content (simple text reading) | COMMENT |
| LOW | …/other/iso-13485-certification/scripts/gap_analyzer.py | 231 | # Check if any keyword appears in the document | COMMENT |
| LOW | …s/other/hugging-face-jobs/scripts/cot-self-instruct.py | 309 | # Check if majority answer matches original and meets threshold | COMMENT |
| LOW | …ills/other/hugging-face-jobs/scripts/finepdfs-stats.py | 423 | # Print results | STRING |
| LOW | …s/other/labarchive-integration/scripts/setup_config.py | 167 | # Check if config already exists | COMMENT |
| LOW | …end/cli/skills/coding/pymc/scripts/model_comparison.py | 104 | # Check if difference is significant relative to SE | COMMENT |
| LOW | …ding/statistical-analysis/scripts/assumption_checks.py | 453 | # Check if grouped data | COMMENT |
| LOW | …ills/coding/torch_geometric/scripts/visualize_graph.py | 159 | # Check if all edges have their reverse | COMMENT |
| LOW | …/skills/coding/pymoo/scripts/many_objective_example.py | 44 | # Print results summary | COMMENT |
| LOW | …kills/coding/pymoo/scripts/single_objective_example.py | 45 | # Print results | COMMENT |
| LOW | …skills/coding/pymoo/scripts/multi_objective_example.py | 36 | # Print results summary | COMMENT |
| LOW | …/hugging-face-evaluation/scripts/evaluation_manager.py | 128 | # Check if first column looks like benchmark names | COMMENT |
| LOW | …/hugging-face-evaluation/scripts/evaluation_manager.py | 138 | # Check if there are numeric values in the table | COMMENT |
| LOW | …/hugging-face-evaluation/scripts/evaluation_manager.py | 281 | # Check if first column header suggests model names | COMMENT |
| LOW | …/hugging-face-evaluation/scripts/evaluation_manager.py | 286 | # Check if remaining headers look like benchmarks | COMMENT |
| LOW | …/hugging-face-evaluation/scripts/evaluation_manager.py | 301 | # Check if data rows have numeric values in most columns (except first) | COMMENT |
| LOW | …/hugging-face-evaluation/scripts/evaluation_manager.py | 346 | # Check if first column header is empty/generic (indicates benchmarks in rows) | COMMENT |
| LOW | …ining/stable-baselines3/scripts/custom_env_template.py | 135 | # Check if goal is reached | COMMENT |
| LOW | …i/skills/ml-training/pufferlib/scripts/env_template.py | 102 | # Check if episode is done | COMMENT |
| LOW | …ills/biology/synthetic-biology/scripts/gene_circuit.py | 250 | # Check if this is a new steady state | COMMENT |
| LOW | …kills/biology/clinical-imaging/scripts/ciliary_beat.py | 154 | # Check if signal has variance (cilia must be beating) | COMMENT |
| LOW | …s/biology/clinical-imaging/scripts/cosinor_analysis.py | 313 | # Print results | STRING |
| LOW | …cli/skills/biology/deeptools/scripts/validate_files.py | 61 | # Check if start and end are integers | COMMENT |
| LOW | …cli/skills/biology/deeptools/scripts/validate_files.py | 168 | # Check if any files were provided | STRING |
| LOW | …cli/skills/biology/deeptools/scripts/validate_files.py | 180 | # Print results | STRING |
| LOW | …skills/biology/deeptools/scripts/workflow_generator.py | 417 | # Check if workflow was specified | STRING |
| LOW⚡ | …/biology/treatment-plans/scripts/check_completeness.py | 295 | # Read file | STRING |
| 19 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| HIGH | …scientific-schematics/scripts/generate_schematic_ai.py | 0 | return only a user-owned openrouter key, never a managed proxy token. | STRING |
| HIGH | …lls/llm-tools/generate-image/scripts/generate_image.py | 0 | return only a user-owned openrouter key, never a managed proxy token. | STRING |
| HIGH | …g/scientific-slides/scripts/generate_slide_image_ai.py | 0 | return only a user-owned openrouter key, never a managed proxy token. | STRING |
| HIGH | …scientific-schematics/scripts/generate_schematic_ai.py | 0 | keep byok off the synthetic sciences credits proxy if a stale base url leaked in. | STRING |
| HIGH | …lls/llm-tools/generate-image/scripts/generate_image.py | 0 | keep byok off the synthetic sciences credits proxy if a stale base url leaked in. | STRING |
| HIGH | …g/scientific-slides/scripts/generate_slide_image_ai.py | 0 | keep byok off the synthetic sciences credits proxy if a stale base url leaked in. | STRING |
| HIGH | …ls/chemistry/admet-prediction/scripts/drug_likeness.py | 0 | parse input: smiles string or csv file. returns list of (name, mol). | STRING |
| HIGH | …chemistry/admet-prediction/scripts/predict_toxicity.py | 0 | parse input: smiles string or csv file. returns list of (name, mol). | STRING |
| HIGH | …ls/chemistry/admet-prediction/scripts/compare_drugs.py | 0 | parse input: smiles string or csv file. returns list of (name, mol). | STRING |
| HIGH | …iology/molecular-cloning/scripts/restriction_digest.py | 0 | return an uppercase dna string from a fasta file or raw sequence. | STRING |
| HIGH | …ills/biology/molecular-cloning/scripts/simulate_pcr.py | 0 | return an uppercase dna string from a fasta file or raw sequence. | STRING |
| HIGH | …lls/biology/molecular-cloning/scripts/design_crispr.py | 0 | return an uppercase dna string from a fasta file or raw sequence. | STRING |
| HIGH | …ls/biology/molecular-cloning/scripts/design_primers.py | 0 | return an uppercase dna string from a fasta file or raw sequence. | STRING |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| MEDIUM | evals/cadence-harness/prepare.ts | 157 | `# Better search and parallelism backlog\n\nUpdated after each three-run batch. Items stay here when the trajector | CODE |
| MEDIUM | frontend/landing/public/docs/assets/index-Cazmh0hf.js | 49 | `).replace(jb,"")}function ap(e,t){return t=ip(t),ip(e)===t}function Be(e,t,l,i,u,s){switch(l){case"children":typeof i== | CODE |
| MEDIUM | frontend/landing/public/docs/assets/index-Cazmh0hf.js | 140 | `,C1='---\ntitle: "Command reference"\ndescription: "Every openscience subcommand: workspace, run, sessions, models, age | CODE |
| MEDIUM | frontend/landing/public/docs/assets/index-Cazmh0hf.js | 552 | `,D1='---\ntitle: "Sessions & one-shot runs"\ndescription: "One agent conversation: history, tool calls, and a working d | CODE |
| MEDIUM | frontend/landing/public/docs/assets/index-Cazmh0hf.js | 730 | `,N1="https://mintlify.com/docs.json",L1="OpenScience",U1={tabs:[{tab:"Guides",groups:[{group:"Start",pages:["index","qu | CODE |
| MEDIUM | frontend/workspace/e2e/skills.spec.ts | 48 | // top). Kept fixme until the click is made robust against that quirk. | COMMENT |
| MEDIUM | backend/cli/test/tool/question.test.ts | 73 | // header: "This Header is Definitely More Than Thirty Characters Long", | COMMENT |
| MEDIUM | …cli/skills/research/research-lookup/research_lookup.py | 143 | return f"""You are an expert research assistant. Please provide comprehensive, accurate research information for | CODE |
| MEDIUM | …ls/research/research-lookup/scripts/research_lookup.py | 143 | return f"""You are an expert research assistant. Please provide comprehensive, accurate research information for | CODE |
| MEDIUM | …et-research-reports/scripts/generate_market_visuals.py | 15 | # Generate all 28 visuals (for comprehensive coverage) | STRING |
| MEDIUM | …scientific-schematics/scripts/generate_schematic_ai.py | 115 | # Scientific diagram best practices prompt template | COMMENT |
| MEDIUM | …ills/visualization/matplotlib/scripts/plot_template.py | 317 | """Create a comprehensive figure with multiple subplots.""" | STRING |
| MEDIUM⚡ | …abases/brenda-database/scripts/brenda_visualization.py | 682 | """Generate a comprehensive set of plots for an enzyme.""" | STRING |
| MEDIUM⚡ | …ases/brenda-database/scripts/enzyme_pathway_builder.py | 806 | """Generate a comprehensive pathway report.""" | STRING |
| LOW | …cli/skills/chemistry/molecular-docking/scripts/rank.py | 423 | "composite_score": entry["score"], # just use raw score | CODE |
| MEDIUM⚡ | …chemistry/admet-prediction/scripts/predict_toxicity.py | 69 | # AMES mutagenicity: comprehensive structural alert library (~30 patterns) | COMMENT |
| MEDIUM | …skills/chemistry/rdkit/scripts/molecular_properties.py | 26 | """Calculate comprehensive molecular properties.""" | STRING |
| MEDIUM | …/other/iso-13485-certification/scripts/gap_analyzer.py | 250 | """Generate comprehensive gap analysis report.""" | STRING |
| MEDIUM | …/other/hugging-face-jobs/scripts/generate-responses.py | 94 | """Create a comprehensive dataset card documenting the generation process.""" | STRING |
| MEDIUM | …s/other/hugging-face-jobs/scripts/cot-self-instruct.py | 374 | """Create a comprehensive dataset card.""" | STRING |
| MEDIUM | …/skills/scholar-evaluation/scripts/calculate_scores.py | 148 | """Generate comprehensive evaluation report.""" | STRING |
| MEDIUM | …ding/statistical-analysis/scripts/assumption_checks.py | 186 | # Levene's test (robust to non-normality) | COMMENT |
| MEDIUM | …ding/statistical-analysis/scripts/assumption_checks.py | 533 | # Run comprehensive check | COMMENT |
| MEDIUM | …ogy/treatment-plans/scripts/validate_treatment_plan.py | 179 | """Display comprehensive validation results.""" | STRING |
| MEDIUM | …/biology/flow-cytometry-analysis/scripts/cell_cycle.py | 122 | # Filter out extreme outliers for robust peak detection | COMMENT |
| MEDIUM | …ology/clinical-reports/scripts/validate_case_report.py | 192 | """Generate comprehensive validation report.""" | STRING |
| MEDIUM | …ls/biology/pharmacology-wetlab/scripts/western_blot.py | 84 | # Simple equal-width fallback (robust for most gel images) | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW⚡ | …tion/scientific-visualization/scripts/figure_export.py | 318 | # Example usage | COMMENT |
| LOW | …cli/skills/databases/kegg-database/scripts/kegg_api.py | 242 | # Example usage | COMMENT |
| LOW | …databases/drugbank-database/scripts/drugbank_helper.py | 307 | # Example usage | COMMENT |
| LOW⚡ | …abases/brenda-database/scripts/brenda_visualization.py | 744 | # Example usage | COMMENT |
| LOW⚡ | …ls/databases/brenda-database/scripts/brenda_queries.py | 814 | # Example usage | COMMENT |
| LOW⚡ | …ases/brenda-database/scripts/enzyme_pathway_builder.py | 1014 | # Example usage | COMMENT |
| LOW | …skills/databases/string-database/scripts/string_api.py | 357 | # Example usage | COMMENT |
| LOW | …s/databases/openalex-database/scripts/query_helpers.py | 293 | # Example usage | COMMENT |
| LOW | …databases/openalex-database/scripts/openalex_client.py | 325 | # Example usage | COMMENT |
| LOW | …s/databases/chembl-database/scripts/example_queries.py | 254 | # Example usage | COMMENT |
| LOW | …linicaltrials-database/scripts/query_clinicaltrials.py | 196 | # Example usage | COMMENT |
| LOW | …ases/opentargets-database/scripts/query_opentargets.py | 369 | # Example usage | STRING |
| LOW | …end/cli/skills/coding/pymc/scripts/model_comparison.py | 358 | # Example usage | STRING |
| LOW | …nd/cli/skills/coding/pymc/scripts/model_diagnostics.py | 328 | # Example usage | COMMENT |
| LOW | …ding/statistical-analysis/scripts/assumption_checks.py | 521 | # Example usage | COMMENT |
| LOW | …nd/cli/skills/coding/simpy/scripts/resource_monitor.py | 320 | # Example usage | COMMENT |
| LOW | …lls/coding/scikit-learn/scripts/clustering_analysis.py | 338 | # Example usage | COMMENT |
| LOW | …coding/scikit-learn/scripts/classification_pipeline.py | 230 | # Example usage | COMMENT |
| LOW⚡ | …g/prime-intellect-lab/templates/basic_rl_training.toml | 4 | # Usage: | COMMENT |
| LOW | …decision-support/scripts/generate_survival_analysis.py | 433 | # Example usage: | COMMENT |
| LOW | …ical-decision-support/scripts/validate_cds_document.py | 323 | # Example usage: | COMMENT |
| LOW | …nical-decision-support/scripts/biomarker_classifier.py | 375 | # Example usage: | COMMENT |
| LOW | …inical-decision-support/scripts/build_decision_tree.py | 412 | # Example usage: | COMMENT |
| LOW | …nical-decision-support/scripts/create_cohort_tables.py | 501 | # Example usage: | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| MEDIUM | frontend/landing/public/docs/assets/index-Cazmh0hf.js | 87 | ## Create a custom agent | COMMENT |
| MEDIUM | …ls/chemistry/molecule-visualization/scripts/draw_2d.py | 106 | # Create the drawer | COMMENT |
| MEDIUM | …ls/chemistry/hypogenic/references/config_template.yaml | 116 | # Define a custom function in your code to parse specific output formats | COMMENT |
| MEDIUM | …ering/hugging-face-datasets/scripts/dataset_manager.py | 53 | # Create a basic README.md with metadata if it doesn't exist | COMMENT |
| MEDIUM | …ering/hugging-face-datasets/scripts/dataset_manager.py | 286 | # Create a newline-delimited JSON string | COMMENT |
| MEDIUM | …ills/coding/torch_geometric/scripts/visualize_graph.py | 155 | # Create a set of edges and reverse edges | COMMENT |
| MEDIUM | …/skills/coding/pymoo/scripts/many_objective_example.py | 19 | # Define the problem - DTLZ2 with 5 objectives | COMMENT |
| MEDIUM | …kills/coding/pymoo/scripts/single_objective_example.py | 21 | # Define the problem - Sphere function (sum of squares) | COMMENT |
| MEDIUM | …skills/coding/pymoo/scripts/multi_objective_example.py | 18 | # Define the problem - ZDT1 (bi-objective) | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| HIGH | …ing/hugging-face-evaluation/scripts/test_extraction.py | 15 | Run from the scripts/ directory: cd scripts && uv run test_extraction.py | STRING |
| HIGH | …/hugging-face-model-trainer/scripts/convert_to_gguf.py | 70 | print(" macOS: xcode-select --install && brew install cmake") | CODE |
| HIGH | …/hugging-face-model-trainer/scripts/convert_to_gguf.py | 27 | - Ubuntu/Debian: sudo apt-get update && sudo apt-get install -y build-essential cmake | STRING |
| HIGH | …/hugging-face-model-trainer/scripts/convert_to_gguf.py | 29 | - macOS: xcode-select --install && brew install cmake | STRING |
| HIGH | …/biology/treatment-plans/scripts/check_completeness.py | 265 | python check_completeness.py plan.tex && echo "Complete" | CODE |
| HIGH | …ogy/treatment-plans/scripts/validate_treatment_plan.py | 316 | python validate_treatment_plan.py plan.tex && echo "Quality check passed" | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | frontend/ui/src/components/line-comment.tsx | 102 | "placeholder", | CODE |
| LOW | frontend/ui/src/components/select.tsx | 28 | "placeholder", | CODE |
| LOW | …nd/workspace/src/components/prompt-placeholder.test.ts | 25 | expect(source).not.toContain('setStore("placeholder"') | CODE |
| LOW | …rkspace/src/components/settings/network-domain.test.ts | 16 | "user@example.org", | CODE |
| LOW | backend/cli/test/tool/research-contract.test.ts | 134 | metric: { name: "placeholder", value: 0, direction: "maximize", baseline: 0, target: 0, unit: "none" }, | CODE |
| LOW | backend/cli/skills/llm-tools/dspy/SKILL.md | 355 | print(result.person.name) # "John Doe" | CODE |
| LOW | backend/cli/skills/llm-tools/dspy/references/modules.md | 236 | print(result.person.name) # "John Doe" | CODE |
| LOW | …nd/cli/skills/llm-tools/langchain/references/agents.md | 137 | ("placeholder", "{agent_scratchpad}"), | CODE |
| LOW | backend/cli/skills/llm-tools/outlines/SKILL.md | 75 | print(user.name) # "John Doe" | CODE |
| LOW | backend/cli/skills/llm-tools/instructor/SKILL.md | 67 | print(user.name) # "John Doe" | CODE |
| LOW | backend/cli/skills/llm-tools/instructor/SKILL.md | 633 | "name": "John Doe", | STRING |
| LOW | backend/cli/skills/llm-tools/instructor/SKILL.md | 675 | "name": "John Doe", | CODE |
| LOW | …s/databases/cosmic-database/scripts/download_cosmic.py | 13 | email="user@example.com", | STRING |
| LOW | …/writing/pptx-posters/assets/poster_html_template.html | 206 | <div id="chart1" class="placeholder" style="width: 100%; height: 400pt;"></div> | CODE |
| LOW | …riting/pptx-posters/assets/poster_quality_checklist.md | 15 | - [ ] No placeholder text remaining (TODO, Lorem ipsum, etc.) | CODE |
| LOW | backend/cli/skills/writing/latex-posters/SKILL.md | 1075 | - [ ] No placeholder text remaining (Lorem ipsum, TODO, etc.) | CODE |
| LOW | …/skills/writing/latex-posters/scripts/review_poster.sh | 179 | echo " [ ] No placeholder text (Lorem ipsum, TODO, etc.)" | CODE |
| LOW | …iting/latex-posters/assets/poster_quality_checklist.md | 15 | - [ ] No placeholder text remaining (TODO, Lorem ipsum, etc.) | CODE |
| LOW | backend/cli/skills/writing/ml-paper-writing/SKILL.md | 604 | % - Lorem ipsum or placeholder text | CODE |
| LOW | backend/cli/src/auth/index.ts | 10 | export const OAUTH_DUMMY_KEY = "synsc-oauth-dummy-key" | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | …lls/databases/fred-economic-data/scripts/fred_query.py | 113 | CODE | |
| LOW | …lls/databases/fred-economic-data/scripts/fred_query.py | 162 | CODE | |
| LOW | …linicaltrials-database/scripts/query_clinicaltrials.py | 22 | CODE | |
| LOW | …cli/skills/chemistry/molecular-docking/scripts/dock.py | 541 | CODE | |
| LOW | …cli/skills/chemistry/molecular-docking/scripts/dock.py | 811 | CODE | |
| LOW | …/other/hugging-face-jobs/scripts/generate-responses.py | 168 | CODE | |
| LOW | …ills/coding/torch_geometric/scripts/visualize_graph.py | 27 | CODE | |
| LOW | …ing/hugging-face-evaluation/scripts/inspect_vllm_uv.py | 49 | CODE | |
| LOW | …g/hugging-face-evaluation/scripts/lighteval_vllm_uv.py | 45 | CODE | |
| LOW | …l-training/stable-baselines3/scripts/train_rl_agent.py | 24 | CODE | |
| LOW | …ls/biology/molecular-cloning/scripts/design_primers.py | 87 | CODE | |
| LOW | …nical-decision-support/scripts/create_cohort_tables.py | 416 | CODE | |
| LOW | …y/neuropixels-analysis/scripts/preprocess_recording.py | 15 | CODE | |
| LOW | …s/biology/pharmacology-wetlab/scripts/dose_response.py | 215 | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| HIGH | backend/cli/skills/ml-training/deepspeed/SKILL.md | 65 | **Pattern 7:** DeepSpeed Configuration JSON Contents Batch Size Related Parameters Optimizer Parameters Scheduler Parame | CODE |
| HIGH | backend/cli/skills/ml-training/pytorch-fsdp/SKILL.md | 35 | **Pattern 2:** Distributed communication package - torch.distributed# Created On: Jul 12, 2017 | Last Updated On: Sep 04 | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| HIGH | backend/cli/skills/writing/latex-posters/SKILL.md | 113 | The #1 issue with AI-generated poster graphics is **TOO MUCH CONTENT**. This causes: | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | …tion/scientific-visualization/scripts/style_presets.py | 195 | def set_color_palette(palette_name: str = 'okabe_ito') -> None: | CODE |
| LOW | …/other/hugging-face-jobs/scripts/generate-responses.py | 61 | logger = logging.getLogger(__name__) | CODE |
| LOW | …s/other/hugging-face-jobs/scripts/cot-self-instruct.py | 75 | logger = logging.getLogger(__name__) | CODE |
| LOW | …ills/other/hugging-face-jobs/scripts/finepdfs-stats.py | 53 | logger = logging.getLogger(__name__) | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| MEDIUM | …/hugging-face-datasets/examples/training_examples.json | 111 | "content": "Great! I've fixed the missing config file issue. Your Node.js app should now start without crashing. | CODE |