Turn any AI agent into an AI Scientist. The #1 Agent Skills library for science, used by 160,000+ scientists worldwide. 140 ready-to-use skills plus 100+ scientific databases covering biology, chemistry, medicine, and drug discovery. Compatible with Cursor, Claude Code, Codex, Pi, Antigravity, and the open Agent Skills standard.
This report presents the forensic synthetic code analysis of K-Dense-AI/scientific-agent-skills, a Python project with 30,878 GitHub stars. SynthScan v2.0 examined 479,917 lines of code across 1322 source files, recording 2713 pattern matches distributed across 20 syntactic categories. The overall adjusted score of 11.6 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).
This chart maps the temporal evolution of the adjusted synthetic code score across successive scan runs. An upward trajectory indicates ongoing incorporation of AI-generated code or expanding LLM-assisted scaffolding; a stable or declining trajectory may reflect active human refactoring, code removal, or the adoption of stricter authorship policies. The dashed secondary line (right axis) independently tracks total raw pattern hit count, which can diverge from the normalised score when codebase size changes significantly between scans.
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 2713 distinct pattern matches across 20 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 |
|---|---|---|---|---|
| HIGH | …scientific-schematics/scripts/generate_schematic_ai.py | 0 | ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: | STRING |
| HIGH | …s/citation-management/scripts/generate_schematic_ai.py | 0 | ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: | STRING |
| HIGH | skills/markitdown/scripts/generate_schematic_ai.py | 0 | ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: | STRING |
| HIGH | skills/pptx-posters/scripts/generate_schematic_ai.py | 0 | ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: | STRING |
| HIGH | skills/treatment-plans/scripts/generate_schematic_ai.py | 0 | ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: | STRING |
| HIGH | …ls/scientific-writing/scripts/generate_schematic_ai.py | 0 | ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: | STRING |
| HIGH | …ical-decision-support/scripts/generate_schematic_ai.py | 0 | ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: | STRING |
| HIGH | …lls/literature-review/scripts/generate_schematic_ai.py | 0 | ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: | STRING |
| HIGH | …ls/scholar-evaluation/scripts/generate_schematic_ai.py | 0 | ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: | STRING |
| HIGH | skills/latex-posters/scripts/generate_schematic_ai.py | 0 | ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: | STRING |
| HIGH | skills/venue-templates/scripts/generate_schematic_ai.py | 0 | ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: | STRING |
| HIGH | …ills/clinical-reports/scripts/generate_schematic_ai.py | 0 | ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: | STRING |
| HIGH | …lls/scientific-slides/scripts/generate_schematic_ai.py | 0 | ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: | STRING |
| HIGH | …hypothesis-generation/scripts/generate_schematic_ai.py | 0 | ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: | STRING |
| HIGH | skills/peer-review/scripts/generate_schematic_ai.py | 0 | ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: | STRING |
| HIGH | …scientific-schematics/scripts/generate_schematic_ai.py | 0 | load .env file from current directory or script directory only. | STRING |
| HIGH | …s/citation-management/scripts/generate_schematic_ai.py | 0 | load .env file from current directory or script directory only. | STRING |
| HIGH | skills/markitdown/scripts/generate_schematic_ai.py | 0 | load .env file from current directory or script directory only. | STRING |
| HIGH | skills/infographics/scripts/generate_infographic_ai.py | 0 | load .env file from current directory or script directory only. | STRING |
| HIGH | skills/pptx-posters/scripts/generate_schematic_ai.py | 0 | load .env file from current directory or script directory only. | STRING |
| HIGH | skills/treatment-plans/scripts/generate_schematic_ai.py | 0 | load .env file from current directory or script directory only. | STRING |
| HIGH | …ls/scientific-writing/scripts/generate_schematic_ai.py | 0 | load .env file from current directory or script directory only. | STRING |
| HIGH | …ical-decision-support/scripts/generate_schematic_ai.py | 0 | load .env file from current directory or script directory only. | STRING |
| HIGH | …lls/literature-review/scripts/generate_schematic_ai.py | 0 | load .env file from current directory or script directory only. | STRING |
| HIGH | …ls/scholar-evaluation/scripts/generate_schematic_ai.py | 0 | load .env file from current directory or script directory only. | STRING |
| HIGH | skills/latex-posters/scripts/generate_schematic_ai.py | 0 | load .env file from current directory or script directory only. | STRING |
| HIGH | skills/venue-templates/scripts/generate_schematic_ai.py | 0 | load .env file from current directory or script directory only. | STRING |
| HIGH | …ills/clinical-reports/scripts/generate_schematic_ai.py | 0 | load .env file from current directory or script directory only. | STRING |
| HIGH | …lls/scientific-slides/scripts/generate_schematic_ai.py | 0 | load .env file from current directory or script directory only. | STRING |
| HIGH | …s/scientific-slides/scripts/generate_slide_image_ai.py | 0 | load .env file from current directory or script directory only. | STRING |
| HIGH | …hypothesis-generation/scripts/generate_schematic_ai.py | 0 | load .env file from current directory or script directory only. | STRING |
| HIGH | skills/peer-review/scripts/generate_schematic_ai.py | 0 | load .env file from current directory or script directory only. | STRING |
| HIGH | …scientific-schematics/scripts/generate_schematic_ai.py | 0 | generate scientific schematics using ai with smart iterative refinement. uses gemini 3.1 pro preview for quality review | STRING |
| HIGH | …s/citation-management/scripts/generate_schematic_ai.py | 0 | generate scientific schematics using ai with smart iterative refinement. uses gemini 3.1 pro preview for quality review | STRING |
| HIGH | skills/markitdown/scripts/generate_schematic_ai.py | 0 | generate scientific schematics using ai with smart iterative refinement. uses gemini 3.1 pro preview for quality review | STRING |
| HIGH | skills/pptx-posters/scripts/generate_schematic_ai.py | 0 | generate scientific schematics using ai with smart iterative refinement. uses gemini 3.1 pro preview for quality review | STRING |
| HIGH | skills/treatment-plans/scripts/generate_schematic_ai.py | 0 | generate scientific schematics using ai with smart iterative refinement. uses gemini 3.1 pro preview for quality review | STRING |
| HIGH | …ls/scientific-writing/scripts/generate_schematic_ai.py | 0 | generate scientific schematics using ai with smart iterative refinement. uses gemini 3.1 pro preview for quality review | STRING |
| HIGH | …ical-decision-support/scripts/generate_schematic_ai.py | 0 | generate scientific schematics using ai with smart iterative refinement. uses gemini 3.1 pro preview for quality review | STRING |
| HIGH | …lls/literature-review/scripts/generate_schematic_ai.py | 0 | generate scientific schematics using ai with smart iterative refinement. uses gemini 3.1 pro preview for quality review | STRING |
| HIGH | …ls/scholar-evaluation/scripts/generate_schematic_ai.py | 0 | generate scientific schematics using ai with smart iterative refinement. uses gemini 3.1 pro preview for quality review | STRING |
| HIGH | skills/latex-posters/scripts/generate_schematic_ai.py | 0 | generate scientific schematics using ai with smart iterative refinement. uses gemini 3.1 pro preview for quality review | STRING |
| HIGH | skills/venue-templates/scripts/generate_schematic_ai.py | 0 | generate scientific schematics using ai with smart iterative refinement. uses gemini 3.1 pro preview for quality review | STRING |
| HIGH | …ills/clinical-reports/scripts/generate_schematic_ai.py | 0 | generate scientific schematics using ai with smart iterative refinement. uses gemini 3.1 pro preview for quality review | STRING |
| HIGH | …lls/scientific-slides/scripts/generate_schematic_ai.py | 0 | generate scientific schematics using ai with smart iterative refinement. uses gemini 3.1 pro preview for quality review | STRING |
| HIGH | …hypothesis-generation/scripts/generate_schematic_ai.py | 0 | generate scientific schematics using ai with smart iterative refinement. uses gemini 3.1 pro preview for quality review | STRING |
| HIGH | skills/peer-review/scripts/generate_schematic_ai.py | 0 | generate scientific schematics using ai with smart iterative refinement. uses gemini 3.1 pro preview for quality review | STRING |
| HIGH | …scientific-schematics/scripts/generate_schematic_ai.py | 0 | create a high-quality scientific diagram with these requirements: visual quality: - clean white or light background (no | STRING |
| HIGH | …s/citation-management/scripts/generate_schematic_ai.py | 0 | create a high-quality scientific diagram with these requirements: visual quality: - clean white or light background (no | STRING |
| HIGH | skills/markitdown/scripts/generate_schematic_ai.py | 0 | create a high-quality scientific diagram with these requirements: visual quality: - clean white or light background (no | STRING |
| HIGH | skills/pptx-posters/scripts/generate_schematic_ai.py | 0 | create a high-quality scientific diagram with these requirements: visual quality: - clean white or light background (no | STRING |
| HIGH | skills/treatment-plans/scripts/generate_schematic_ai.py | 0 | create a high-quality scientific diagram with these requirements: visual quality: - clean white or light background (no | STRING |
| HIGH | …ls/scientific-writing/scripts/generate_schematic_ai.py | 0 | create a high-quality scientific diagram with these requirements: visual quality: - clean white or light background (no | STRING |
| HIGH | …ical-decision-support/scripts/generate_schematic_ai.py | 0 | create a high-quality scientific diagram with these requirements: visual quality: - clean white or light background (no | STRING |
| HIGH | …lls/literature-review/scripts/generate_schematic_ai.py | 0 | create a high-quality scientific diagram with these requirements: visual quality: - clean white or light background (no | STRING |
| HIGH | …ls/scholar-evaluation/scripts/generate_schematic_ai.py | 0 | create a high-quality scientific diagram with these requirements: visual quality: - clean white or light background (no | STRING |
| HIGH | skills/latex-posters/scripts/generate_schematic_ai.py | 0 | create a high-quality scientific diagram with these requirements: visual quality: - clean white or light background (no | STRING |
| HIGH | skills/venue-templates/scripts/generate_schematic_ai.py | 0 | create a high-quality scientific diagram with these requirements: visual quality: - clean white or light background (no | STRING |
| HIGH | …ills/clinical-reports/scripts/generate_schematic_ai.py | 0 | create a high-quality scientific diagram with these requirements: visual quality: - clean white or light background (no | STRING |
| HIGH | …lls/scientific-slides/scripts/generate_schematic_ai.py | 0 | create a high-quality scientific diagram with these requirements: visual quality: - clean white or light background (no | STRING |
| 243 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | scan_pr_skills.py | 63 | except Exception as exc: # pragma: no cover - defensive | CODE |
| LOW | scan_pr_skills.py | 84 | except Exception as exc: # pragma: no cover - defensive | CODE |
| LOW | scan_skills.py | 174 | except Exception as e: | CODE |
| LOW | scan_skills.py | 198 | except Exception as e: | CODE |
| LOW | …lls/benchling-integration/references/authentication.md | 328 | except Exception as e: | CODE |
| MEDIUM | skills/networkx/references/io.md | 447 | print(f"Error reading GraphML: {e}") | CODE |
| LOW | skills/research-lookup/scripts/research_lookup.py | 936 | except Exception as exc: | CODE |
| LOW | skills/research-lookup/scripts/research_lookup.py | 951 | except Exception as fallback_exc: | CODE |
| LOW | skills/research-lookup/scripts/research_lookup.py | 1167 | except Exception as exc: | STRING |
| MEDIUM | skills/research-lookup/scripts/research_lookup.py | 1168 | print(f"Error: {exc}", file=sys.stderr) | STRING |
| MEDIUM⚡ | skills/shap/references/workflows.md | 70 | print(f"Error rate: {len(error_indices) / len(y_test):.2%}") | CODE |
| LOW | skills/dask/references/futures.md | 499 | except Exception as e: | CODE |
| LOW | skills/dask/references/futures.md | 533 | except Exception: | CODE |
| LOW | …ls/get-available-resources/scripts/detect_resources.py | 40 | except Exception: | CODE |
| LOW | …ls/get-available-resources/scripts/detect_resources.py | 75 | except Exception as e: | CODE |
| LOW | …ls/get-available-resources/scripts/detect_resources.py | 195 | except Exception: | CODE |
| LOW | …ls/get-available-resources/scripts/detect_resources.py | 199 | except Exception: | CODE |
| LOW | …ills/exploratory-data-analysis/scripts/eda_analyzer.py | 209 | except Exception as e: | CODE |
| MEDIUM | …ills/exploratory-data-analysis/scripts/eda_analyzer.py | 210 | print(f"Error loading reference: {e}", file=sys.stderr) | CODE |
| LOW | …ills/exploratory-data-analysis/scripts/eda_analyzer.py | 245 | except Exception as e: | CODE |
| LOW | …ills/exploratory-data-analysis/scripts/eda_analyzer.py | 329 | except Exception as e: | CODE |
| LOW | …ills/exploratory-data-analysis/scripts/eda_analyzer.py | 375 | except Exception as e: | CODE |
| LOW | …ills/exploratory-data-analysis/scripts/eda_analyzer.py | 415 | except Exception as e: | CODE |
| MEDIUM | …ills/exploratory-data-analysis/scripts/eda_analyzer.py | 529 | print(f"Error: File not found: {filepath}") | CODE |
| LOW | skills/iso-13485-certification/scripts/gap_analyzer.py | 217 | except Exception as e: | CODE |
| LOW | skills/esm/references/forge-api.md | 363 | except Exception as e: | CODE |
| MEDIUM | skills/esm/references/forge-api.md | 364 | print(f"Error processing {i}: {e}") | CODE |
| LOW | skills/esm/references/forge-api.md | 404 | except Exception as e: | CODE |
| LOW | skills/esm/references/forge-api.md | 582 | except Exception as e: | CODE |
| LOW | skills/esm/references/forge-api.md | 641 | except Exception as e: | CODE |
| MEDIUM | …scientific-schematics/scripts/generate_schematic_ai.py | 33 | print("Error: requests library not found. Install with: pip install requests") | CODE |
| LOW | …scientific-schematics/scripts/generate_schematic_ai.py | 288 | except Exception as e: | CODE |
| LOW | …scientific-schematics/scripts/generate_schematic_ai.py | 391 | except Exception as e: | CODE |
| LOW | …scientific-schematics/scripts/generate_schematic_ai.py | 548 | except Exception as e: | CODE |
| MEDIUM⚡ | …scientific-schematics/scripts/generate_schematic_ai.py | 782 | print("Error: OPENROUTER_API_KEY environment variable not set") | STRING |
| MEDIUM⚡ | …scientific-schematics/scripts/generate_schematic_ai.py | 790 | print("Error: Iterations must be between 1 and 2") | STRING |
| LOW | …scientific-schematics/scripts/generate_schematic_ai.py | 810 | except Exception as e: | STRING |
| MEDIUM⚡ | …ls/scientific-schematics/scripts/generate_schematic.py | 95 | print("Error: OPENROUTER_API_KEY environment variable not set") | STRING |
| MEDIUM⚡ | …ls/scientific-schematics/scripts/generate_schematic.py | 108 | print(f"Error: AI generation script not found: {ai_script}") | STRING |
| LOW | …ls/scientific-schematics/scripts/generate_schematic.py | 132 | except Exception as e: | STRING |
| MEDIUM | …ls/scientific-schematics/scripts/generate_schematic.py | 133 | print(f"Error executing AI generation: {e}") | STRING |
| LOW | skills/pyzotero/references/files-attachments.md | 95 | except Exception as e: | CODE |
| LOW | skills/pyzotero/references/error-handling.md | 45 | except Exception as e: | CODE |
| LOW | skills/pyzotero/references/error-handling.md | 105 | except Exception as e: | CODE |
| LOW | skills/deeptools/scripts/validate_files.py | 72 | except Exception as e: | CODE |
| MEDIUM | skills/medchem/scripts/filter_molecules.py | 23 | print(f"Error: Missing required package: {e}") | CODE |
| MEDIUM | skills/medchem/scripts/filter_molecules.py | 50 | print(f"Error: Column '{smiles_column}' not found") | CODE |
| MEDIUM | skills/medchem/scripts/filter_molecules.py | 65 | print(f"Error: Unsupported file format: {suffix}") | CODE |
| MEDIUM | skills/medchem/scripts/filter_molecules.py | 237 | print("Error: Specify at least one filter (--rules, --query, --pains, --nibr, etc.)") | CODE |
| LOW | skills/fluidsim/references/advanced_features.md | 257 | except Exception as e: | STRING |
| MEDIUM | skills/fluidsim/references/advanced_features.md | 258 | print(f"Error loading {sim_dir}: {e}") | STRING |
| LOW | skills/pymatgen/references/materials_project_api.md | 432 | except Exception as e: | CODE |
| MEDIUM | skills/pymatgen/scripts/structure_analyzer.py | 32 | print("Error: pymatgen is not installed. Install with: pip install pymatgen") | CODE |
| LOW | skills/pymatgen/scripts/structure_analyzer.py | 125 | except Exception as e: | CODE |
| LOW | skills/pymatgen/scripts/structure_analyzer.py | 165 | except Exception as e: | CODE |
| LOW | skills/pymatgen/scripts/structure_analyzer.py | 239 | except Exception as e: | CODE |
| MEDIUM | skills/pymatgen/scripts/structure_analyzer.py | 240 | print(f"Error reading structure file: {e}") | CODE |
| MEDIUM | skills/pymatgen/scripts/structure_analyzer.py | 262 | print("Error: PyYAML is not installed. Install with: pip install pyyaml") | CODE |
| MEDIUM | skills/pymatgen/scripts/structure_converter.py | 27 | print("Error: pymatgen is not installed. Install with: pip install pymatgen") | CODE |
| MEDIUM | skills/pymatgen/scripts/structure_converter.py | 52 | print("Error: Must specify either output_path or output_format") | CODE |
| 612 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | skills/qiskit/references/patterns.md | 27 | ## Step 1: Map | COMMENT |
| LOW | skills/qiskit/references/patterns.md | 116 | ## Step 2: Optimize | COMMENT |
| LOW | skills/qiskit/references/patterns.md | 163 | ## Step 3: Execute | COMMENT |
| LOW | skills/qiskit/references/patterns.md | 259 | ## Step 4: Post-process | COMMENT |
| LOW | skills/shap/SKILL.md | 39 | ### Step 1: Select the Right Explainer | COMMENT |
| LOW | skills/shap/SKILL.md | 60 | ### Step 2: Compute SHAP Values | COMMENT |
| LOW | skills/shap/SKILL.md | 83 | ### Step 3: Visualize Results | COMMENT |
| LOW⚡ | skills/shap/SKILL.md | 135 | # Step 3: Global importance | COMMENT |
| LOW⚡ | skills/shap/SKILL.md | 138 | # Step 4: Feature relationships | COMMENT |
| LOW⚡ | skills/shap/SKILL.md | 141 | # Step 5: Individual explanation | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 24 | # Step 1: Load and split data | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 27 | # Step 2: Train model (example with XGBoost) | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 32 | # Step 3: Create explainer | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 35 | # Step 4: Compute SHAP values | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 38 | # Step 5: Visualize global importance | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 41 | # Step 6: Examine top features in detail | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 45 | # Step 7: Explain individual predictions | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 59 | # Step 1: Compute SHAP values | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 63 | # Step 2: Identify prediction errors | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 68 | # Step 3: Analyze errors | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 72 | # Step 4: Explain misclassified samples | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 78 | # Step 5: Check if model learned correct patterns | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 82 | # Step 6: Investigate specific feature relationships | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 88 | # Step 7: Validate feature interactions | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 120 | # Step 3: Engineer new features based on insights | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 125 | # Step 4: Retrain with engineered features | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 130 | # Step 5: Compare feature importance | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 136 | # Step 6: Validate improvement | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 156 | # Step 1: Train multiple models | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 163 | # Step 2: Compute SHAP values for each model | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 172 | # Step 3: Compare global feature importance | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 175 | # Step 4: Compare model scores | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 180 | # Step 5: Check consistency of feature importance | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 190 | # Step 6: Analyze specific predictions across models | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 196 | # Step 7: Decision based on: | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 214 | # Step 1: Identify protected attributes | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 217 | # Step 2: Compute SHAP values | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 221 | # Step 3: Compare feature importance across groups | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 229 | # Step 4: Check if protected attribute has high SHAP importance | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 234 | # Step 5: Analyze predictions for each group | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 276 | # Step 1: Load or build neural network | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 279 | # Step 2: Select background dataset | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 283 | # Step 3: Create DeepExplainer | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 286 | # Step 4: Compute SHAP values (may take time) | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 291 | # Step 5: Handle multi-output models | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 332 | # Step 1: Train and save model | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 336 | # Step 2: Create and save explainer | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 340 | # Step 3: Create explanation service | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 433 | # Step 1: Prepare data with time-based features | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 441 | # Step 2: Train model | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 446 | # Step 3: Compute SHAP values | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 450 | # Step 4: Analyze temporal patterns | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 454 | # Step 5: Check lagged feature importance | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 460 | # Step 6: Explain specific predictions | COMMENT |
| LOW⚡ | skills/shap/references/workflows.md | 465 | # Step 7: Validate seasonality understanding | COMMENT |
| LOW | skills/shap/references/workflows.md | 104 | # Step 1: Initial model with baseline features | COMMENT |
| LOW | skills/shap/references/workflows.md | 109 | # Step 2: Identify feature engineering opportunities | COMMENT |
| LOW | skills/shap/references/workflows.md | 246 | # Step 6: Check for proxy features | COMMENT |
| LOW | skills/shap/references/workflows.md | 255 | # Step 7: Mitigation strategies if bias found | COMMENT |
| LOW | skills/shap/references/workflows.md | 309 | # Step 6: Visualize | COMMENT |
| 467 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| MEDIUM | skills/pymc/references/workflows.md | 16 | # =============== | COMMENT |
| MEDIUM | skills/pymc/references/workflows.md | 24 | # ============== | COMMENT |
| MEDIUM | skills/pymc/references/workflows.md | 45 | # ========================== | COMMENT |
| MEDIUM | skills/pymc/references/workflows.md | 55 | # ============ | COMMENT |
| MEDIUM | skills/pymc/references/workflows.md | 71 | # ==================== | COMMENT |
| MEDIUM | skills/pymc/references/workflows.md | 93 | # ============================== | COMMENT |
| MEDIUM | skills/pymc/references/workflows.md | 103 | # ================== | COMMENT |
| MEDIUM | skills/pymc/references/workflows.md | 115 | # ============================ | COMMENT |
| MEDIUM | skills/pymc/references/workflows.md | 136 | # =============== | COMMENT |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 16 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 18 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 51 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 53 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 96 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 98 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 112 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 114 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 132 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 134 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 182 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 184 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 198 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 200 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 262 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 264 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 320 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 322 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 16 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 18 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 41 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 43 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 69 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 71 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 85 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 87 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 106 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 108 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 149 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 151 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 165 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 167 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 195 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 197 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 230 | # ============================================================================= | COMMENT |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 232 | # ============================================================================= | COMMENT |
| MEDIUM | skills/onekgpd/scripts/onekgpd_meta.py | 36 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | skills/onekgpd/scripts/onekgpd_meta.py | 38 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | skills/onekgpd/scripts/onekgpd_meta.py | 53 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | skills/onekgpd/scripts/onekgpd_meta.py | 55 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | skills/onekgpd/scripts/onekgpd_meta.py | 90 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | skills/onekgpd/scripts/onekgpd_meta.py | 92 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | skills/onekgpd/scripts/onekgpd_meta.py | 156 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | skills/onekgpd/scripts/onekgpd_meta.py | 158 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | skills/onekgpd/scripts/onekgpd_meta.py | 196 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | skills/onekgpd/scripts/onekgpd_meta.py | 198 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | skills/onekgpd/scripts/onekgpd_meta.py | 426 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | skills/onekgpd/scripts/onekgpd_meta.py | 428 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | skills/onekgpd/scripts/onekgpd_api.py | 47 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | skills/onekgpd/scripts/onekgpd_api.py | 49 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | skills/onekgpd/scripts/onekgpd_api.py | 60 | # --------------------------------------------------------------------------- | COMMENT |
| 118 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW⚡ | tests/test_research_lookup.py | 54 | def test_default_backend_is_search_and_parallel_alias_is_research(self, _which): | CODE |
| LOW⚡ | tests/test_research_lookup.py | 63 | def test_chat_is_available_but_never_selected_by_default(self, _which): | CODE |
| LOW⚡ | tests/test_research_lookup.py | 72 | def test_explicit_chat_preserves_content_basis_and_citations(self, _which): | CODE |
| LOW | tests/test_research_lookup.py | 124 | def test_parser_and_class_default_to_sixty_references(self, _which): | CODE |
| LOW | tests/test_research_lookup.py | 138 | def test_nonacademic_lookup_uses_one_search_without_extract(self, _which): | CODE |
| LOW | tests/test_research_lookup.py | 164 | def test_academic_lookup_runs_facets_and_batched_extract(self, _which): | CODE |
| LOW | tests/test_research_lookup.py | 234 | def test_perplexity_failure_fallback_is_opt_in(self, _which): | CODE |
| LOW | tests/test_research_lookup.py | 258 | def test_deduplication_merges_doi_url_and_title_records(self): | CODE |
| LOW | tests/test_research_lookup.py | 281 | def test_packet_has_manuscript_artifacts_and_never_pads_shortfall(self): | CODE |
| LOW | tests/test_research_lookup.py | 314 | def test_retracted_reference_is_marked_for_exclusion(self): | CODE |
| LOW | tests/test_research_lookup.py | 337 | def test_save_packet_writes_all_expected_artifacts(self): | CODE |
| LOW | tests/test_research_lookup.py | 369 | def test_existing_citation_extraction_remains_available(self): | CODE |
| LOW | skills/qiskit/references/patterns.md | 449 | def cost_function_with_tracking(params): | CODE |
| LOW | skills/pymc/scripts/model_comparison.py | 293 | def cross_validation_comparison(models_dict: Dict[str, Any], | CODE |
| LOW | skills/research-lookup/scripts/research_lookup.py | 370 | def _rank_sources_for_extraction( | CODE |
| LOW | skills/research-lookup/scripts/research_lookup.py | 884 | def _extract_citations_from_text(text: str) -> list[dict[str, str]]: | CODE |
| LOW | skills/geomaster/references/scientific-domains.md | 14 | def coastal_vulnerability_index(dem_path, shoreline_path, output_path): | CODE |
| LOW | skills/geomaster/references/scientific-domains.md | 350 | def estimate_biomass_from_lidar(chm_path, plot_data): | CODE |
| LOW | skills/geomaster/references/industry-applications.md | 221 | def power_line_corridor_analysis(power_lines_path, vegetation_height_path, buffer_distance=50): | CODE |
| LOW | skills/geomaster/references/advanced-gis.md | 176 | def emerging_hot_spot_analysis(cube, k=8): | CODE |
| LOW | skills/geomaster/references/machine-learning.md | 18 | def train_random_forest_classifier(raster_path, training_gdf): | CODE |
| LOW | skills/onekgpd/scripts/onekgpd_meta.py | 272 | def cmd_list_superpopulations(args) -> None: | CODE |
| LOW | skills/onekgpd/scripts/onekgpd_meta.py | 328 | def cmd_superpopulation_summary(args) -> None: | CODE |
| LOW | skills/onekgpd/scripts/onekgpd_meta.py | 376 | def cmd_select_samples_by_population(args) -> None: | CODE |
| LOW | skills/onekgpd/scripts/onekgpd_api.py | 442 | def cmd_count_variants_in_samples(args) -> None: | CODE |
| LOW | skills/onekgpd/scripts/onekgpd_api.py | 450 | def cmd_select_variants_in_samples(args) -> None: | CODE |
| LOW | skills/onekgpd/scripts/onekgpd_api.py | 539 | def cmd_count_samples_hom_ref(args) -> None: | CODE |
| LOW | skills/onekgpd/scripts/onekgpd_api.py | 568 | def cmd_select_samples_hom_ref(args) -> None: | CODE |
| LOW | skills/dask/references/dataframes.md | 140 | def custom_partition_function(partition_df): | CODE |
| LOW | …ills/exploratory-data-analysis/scripts/eda_analyzer.py | 251 | def analyze_general_scientific(filepath, extension): | CODE |
| LOW | skills/experimental-design/scripts/randomization.py | 89 | def stratified_block_randomization(strata, arms=("treatment", "control"), | CODE |
| LOW | skills/iso-13485-certification/scripts/gap_analyzer.py | 291 | def _generate_recommendations(self, missing_procedures: List[Dict], | CODE |
| LOW | skills/esm/references/workflows.md | 475 | def predict_function_generative(sequence): | CODE |
| LOW | skills/esm/references/workflows.md | 491 | def predict_function_embedding(sequence, function_classifier): | CODE |
| LOW | skills/esm/references/esm3-api.md | 318 | def generate_with_temperature_schedule(model, protein, temperatures): | CODE |
| LOW | skills/esm/references/esm-c-api.md | 129 | def batch_encode_variable_length(model, sequences, max_batch_size=32): | CODE |
| LOW | skills/esm/references/esm-c-api.md | 366 | def get_per_residue_embeddings(model, sequence): | CODE |
| LOW | skills/esm/references/esm-c-api.md | 412 | def efficient_batch_processing(model, sequences, batch_size=32): | CODE |
| LOW | …scientific-schematics/scripts/generate_schematic_ai.py | 214 | def _extract_image_from_response(self, response: Dict[str, Any]) -> Optional[bytes]: | CODE |
| LOW | skills/deeptools/scripts/workflow_generator.py | 85 | def generate_chipseq_qc_workflow(output_file, params): | CODE |
| LOW | skills/deeptools/scripts/workflow_generator.py | 162 | def generate_chipseq_analysis_workflow(output_file, params): | STRING |
| LOW | skills/deeptools/scripts/workflow_generator.py | 283 | def generate_rnaseq_coverage_workflow(output_file, params): | STRING |
| LOW | skills/deeptools/scripts/workflow_generator.py | 334 | def generate_atacseq_workflow(output_file, params): | STRING |
| LOW | skills/fluidsim/references/advanced_features.md | 291 | def _complete_params_with_default(params): | CODE |
| LOW | …s/citation-management/scripts/generate_schematic_ai.py | 214 | def _extract_image_from_response(self, response: Dict[str, Any]) -> Optional[bytes]: | CODE |
| LOW | …ills/citation-management/scripts/validate_citations.py | 303 | def parse_manuscript_citations(self, filepath: str) -> List[str]: | CODE |
| LOW⚡ | skills/citation-management/scripts/search_pubmed.py | 154 | def _extract_metadata_from_xml(self, article: ET.Element) -> Optional[Dict]: | CODE |
| LOW | skills/markitdown/scripts/generate_schematic_ai.py | 214 | def _extract_image_from_response(self, response: Dict[str, Any]) -> Optional[bytes]: | CODE |
| LOW | skills/markitdown/scripts/convert_literature.py | 19 | def extract_metadata_from_filename(filename: str) -> Dict[str, str]: | CODE |
| LOW | skills/pytdc/scripts/benchmark_evaluation.py | 43 | def single_dataset_evaluation(group, dataset_name='Caco2_Wang'): | CODE |
| LOW | skills/pytdc/scripts/benchmark_evaluation.py | 102 | def multiple_datasets_evaluation(group): | CODE |
| LOW | skills/pytdc/scripts/benchmark_evaluation.py | 247 | def leaderboard_submission_guide(): | STRING |
| LOW | skills/pytdc/scripts/molecular_generation.py | 156 | def goal_directed_generation_template(): | CODE |
| LOW | skills/pytdc/scripts/molecular_generation.py | 220 | def distribution_learning_example(train_smiles): | STRING |
| LOW | skills/pytdc/scripts/molecular_generation.py | 309 | def constraint_satisfaction_example(): | STRING |
| LOW | skills/xlsx/scripts/office/validators/docx.py | 66 | def validate_whitespace_preservation(self): | CODE |
| LOW | skills/xlsx/scripts/office/validators/docx.py | 163 | def count_paragraphs_in_unpacked(self): | CODE |
| LOW⚡ | skills/xlsx/scripts/office/validators/docx.py | 179 | def count_paragraphs_in_original(self): | CODE |
| LOW | skills/xlsx/scripts/office/validators/redlining.py | 198 | def _remove_author_tracked_changes(self, root): | CODE |
| LOW | skills/xlsx/scripts/office/validators/pptx.py | 104 | def validate_slide_layout_ids(self): | CODE |
| 302 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| HIGH | SECURITY.md | 1474 | > The references/data-sources.md file contains multiple code examples using placeholder API key variables (YOUR_API_KE | CODE |
| HIGH | …lls/benchling-integration/references/authentication.md | 301 | -u "your_api_key:" \ | CODE |
| HIGH | …lls/benchling-integration/references/authentication.md | 321 | auth_method=ApiKeyAuth("your_api_key") | CODE |
| HIGH | …lls/benchling-integration/references/authentication.md | 381 | auth_method=ApiKeyAuth("your_api_key"), | CODE |
| HIGH | …ills/benchling-integration/references/api_endpoints.md | 26 | -u "your_api_key:" | CODE |
| HIGH | …ills/benchling-integration/references/sdk_reference.md | 571 | auth_method=ApiKeyAuth("your_api_key"), | CODE |
| HIGH | …ills/benchling-integration/references/sdk_reference.md | 578 | auth_method=ApiKeyAuth("your_api_key"), | CODE |
| HIGH | skills/geomaster/references/data-sources.md | 179 | 'key': YOUR_API_KEY | STRING |
| HIGH | skills/geomaster/references/data-sources.md | 208 | 'appid': YOUR_API_KEY | STRING |
| HIGH⚡ | …scientific-schematics/scripts/generate_schematic_ai.py | 784 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH⚡ | …ls/scientific-schematics/scripts/generate_schematic.py | 99 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH | skills/pyzotero/SKILL.md | 27 | ZOTERO_API_KEY=your_api_key | CODE |
| HIGH | skills/database-lookup/references/bea.md | 13 | - Pass as query parameter: `&UserID=YOUR_API_KEY` | CODE |
| HIGH | skills/database-lookup/references/lincs-l1000.md | 13 | - Pass via header: `user_key: YOUR_API_KEY` | CODE |
| HIGH⚡ | skills/database-lookup/references/lincs-l1000.md | 36 | curl -H "user_key: YOUR_API_KEY" \ | CODE |
| HIGH⚡ | skills/database-lookup/references/lincs-l1000.md | 40 | curl -H "user_key: YOUR_API_KEY" \ | CODE |
| HIGH⚡ | skills/database-lookup/references/lincs-l1000.md | 44 | curl -H "user_key: YOUR_API_KEY" \ | CODE |
| HIGH⚡ | skills/database-lookup/references/lincs-l1000.md | 48 | curl -H "user_key: YOUR_API_KEY" \ | CODE |
| HIGH | skills/database-lookup/references/omim.md | 10 | - Pass as query parameter: `?apiKey=YOUR_API_KEY` | CODE |
| HIGH | skills/database-lookup/references/addgene.md | 10 | Pass as: `Authorization: Token <your_api_key>` | CODE |
| HIGH | skills/citation-management/references/pubmed_search.md | 385 | api_key=YOUR_API_KEY | CODE |
| HIGH | skills/citation-management/references/pubmed_search.md | 418 | api_key=YOUR_API_KEY | CODE |
| HIGH | skills/citation-management/references/pubmed_search.md | 442 | api_key=YOUR_API_KEY | CODE |
| HIGH⚡ | …s/citation-management/scripts/generate_schematic_ai.py | 784 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH⚡ | …ills/citation-management/scripts/generate_schematic.py | 99 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH⚡ | skills/markitdown/scripts/generate_schematic_ai.py | 784 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH⚡ | skills/markitdown/scripts/generate_schematic.py | 99 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH | skills/infographics/scripts/generate_infographic_ai.py | 1286 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH⚡ | skills/infographics/scripts/generate_infographic.py | 182 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH⚡ | skills/pptx-posters/scripts/generate_schematic_ai.py | 784 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH⚡ | skills/pptx-posters/scripts/generate_schematic.py | 99 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH⚡ | skills/treatment-plans/scripts/generate_schematic_ai.py | 784 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH⚡ | skills/treatment-plans/scripts/generate_schematic.py | 99 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH⚡ | …ls/scientific-writing/scripts/generate_schematic_ai.py | 784 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH⚡ | skills/scientific-writing/scripts/generate_schematic.py | 99 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH⚡ | skills/scientific-writing/scripts/generate_image.py | 108 | print("OPENROUTER_API_KEY=your-api-key-here") | CODE |
| HIGH⚡ | skills/scientific-writing/scripts/generate_image.py | 110 | print("export OPENROUTER_API_KEY=your-api-key-here") | CODE |
| HIGH⚡ | …ical-decision-support/scripts/generate_schematic_ai.py | 784 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH⚡ | …linical-decision-support/scripts/generate_schematic.py | 99 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH | skills/paper-lookup/references/core.md | 15 | - **Header:** `Authorization: Bearer YOUR_API_KEY` | CODE |
| HIGH | skills/paper-lookup/references/core.md | 16 | - **Query param:** `?api_key=YOUR_API_KEY` | CODE |
| HIGH⚡ | …lls/literature-review/scripts/generate_schematic_ai.py | 784 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH⚡ | skills/literature-review/scripts/generate_schematic.py | 99 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH⚡ | …ls/scholar-evaluation/scripts/generate_schematic_ai.py | 784 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH⚡ | skills/scholar-evaluation/scripts/generate_schematic.py | 99 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH | skills/cirq/references/hardware.md | 173 | # export IONQ_API_KEY=your_api_key | COMMENT |
| HIGH | skills/cirq/references/hardware.md | 493 | export IONQ_API_KEY=your_api_key | CODE |
| HIGH⚡ | skills/latex-posters/scripts/generate_schematic_ai.py | 784 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH⚡ | skills/latex-posters/scripts/generate_schematic.py | 99 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH | skills/adaptyv/SKILL.md | 51 | ADAPTYV_API_KEY=your_api_key | CODE |
| HIGH⚡ | skills/venue-templates/scripts/generate_schematic_ai.py | 784 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH⚡ | skills/venue-templates/scripts/generate_schematic.py | 99 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH | skills/pytorch-lightning/references/logging.md | 103 | api_key="YOUR_API_KEY", | CODE |
| HIGH⚡ | …ills/clinical-reports/scripts/generate_schematic_ai.py | 784 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH⚡ | skills/clinical-reports/scripts/generate_schematic.py | 99 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH⚡ | …lls/scientific-slides/scripts/generate_schematic_ai.py | 784 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH⚡ | …s/scientific-slides/scripts/generate_slide_image_ai.py | 704 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH⚡ | skills/scientific-slides/scripts/generate_schematic.py | 99 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH⚡ | …ills/scientific-slides/scripts/generate_slide_image.py | 96 | print(" export OPENROUTER_API_KEY='your_api_key'") | STRING |
| HIGH | skills/tamarind/SKILL.md | 51 | export TAMARIND_API_KEY="your_api_key" | CODE |
| 9 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| HIGH | skills/research-lookup/scripts/research_lookup.py | 126 | "Find conflicting, contradictory, null, negative, replication, and limitation " | CODE |
| HIGH | skills/xlsx/scripts/office/soffice.py | 150 | if (sv[0] >= 0 && sv[0] < 1024) { | CODE |
| HIGH | skills/xlsx/scripts/office/soffice.py | 169 | if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) { | CODE |
| HIGH | skills/xlsx/scripts/office/soffice.py | 178 | if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) { | CODE |
| HIGH | skills/xlsx/scripts/office/soffice.py | 192 | if (fd >= 0 && fd < 1024 && is_shimmed[fd]) { | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 403 | ...Array(nActual).fill(null), | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 411 | dataUsed.push(step.historical_values[i]); | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 413 | dataUsed.push(null); | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 413 | dataUsed.push(null); | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 427 | if (forecastIdx >= 0 && forecastIdx < nForecast) {{ | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 428 | q90Lower.push(step.q10[forecastIdx]); | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 429 | q90Upper.push(step.q90[forecastIdx]); | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 430 | q80Lower.push(step.q20[forecastIdx]); | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 431 | q80Upper.push(step.q80[forecastIdx]); | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 433 | q90Lower.push(null); | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 433 | q90Lower.push(null); | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 434 | q90Upper.push(null); | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 434 | q90Upper.push(null); | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 435 | q80Lower.push(null); | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 435 | q80Lower.push(null); | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 436 | q80Upper.push(null); | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 436 | q80Upper.push(null); | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 448 | if (forecastIdx >= 0 && forecastIdx < nForecast) {{ | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 449 | forecastData.push(step.point_forecast[forecastIdx]); | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 451 | forecastData.push(null); | CODE |
| HIGH⚡ | …recasting/examples/global-temperature/generate_html.py | 451 | forecastData.push(null); | CODE |
| HIGH | …recasting/examples/global-temperature/generate_html.py | 227 | let chart = null; | CODE |
| HIGH | …recasting/examples/global-temperature/generate_html.py | 229 | let playInterval = null; | CODE |
| HIGH | …recasting/examples/global-temperature/generate_html.py | 275 | data: [...Array(animationData.actual_data.dates.length).fill(null), ...finalStep.point_forec | CODE |
| HIGH | skills/treatment-plans/scripts/check_completeness.py | 257 | python check_completeness.py plan.tex && echo "Complete" | CODE |
| HIGH | …lls/treatment-plans/scripts/validate_treatment_plan.py | 313 | python validate_treatment_plan.py plan.tex && echo "Quality check passed" | CODE |
| HIGH | skills/pptx/scripts/office/soffice.py | 116 | if (sv[0] >= 0 && sv[0] < 1024) { | CODE |
| HIGH | skills/pptx/scripts/office/soffice.py | 135 | if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) { | CODE |
| HIGH | skills/pptx/scripts/office/soffice.py | 144 | if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) { | CODE |
| HIGH | skills/pptx/scripts/office/soffice.py | 158 | if (fd >= 0 && fd < 1024 && is_shimmed[fd]) { | CODE |
| HIGH | skills/pyopenms/scripts/theoretical_spectrum.py | 49 | print(f"Peptide: {seq.toString()} ({len(spec)} fragment peaks)") | CODE |
| HIGH | skills/pyopenms/scripts/mass_calculator.py | 69 | print(f"Peptide: {seq.toString()}") | CODE |
| HIGH | skills/pyopenms/scripts/mass_calculator.py | 70 | print(f"Formula: {formula.toString()}") | CODE |
| HIGH | skills/pyopenms/scripts/mass_calculator.py | 81 | print(f"\nFormula: {formula.toString()}") | CODE |
| HIGH | skills/pyopenms/scripts/digest_protein.py | 74 | pep_str = pep.toString() | CODE |
| HIGH | skills/docx/scripts/office/soffice.py | 116 | if (sv[0] >= 0 && sv[0] < 1024) { | CODE |
| HIGH | skills/docx/scripts/office/soffice.py | 135 | if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) { | CODE |
| HIGH | skills/docx/scripts/office/soffice.py | 144 | if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) { | CODE |
| HIGH | skills/docx/scripts/office/soffice.py | 158 | if (fd >= 0 && fd < 1024 && is_shimmed[fd]) { | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | scan_pr_skills.py | 99 | CODE | |
| LOW | scan_skills.py | 58 | CODE | |
| LOW | skills/pymc/scripts/model_comparison.py | 27 | CODE | |
| LOW | skills/pymc/scripts/model_comparison.py | 120 | CODE | |
| LOW | skills/research-lookup/scripts/manuscript_packet.py | 433 | CODE | |
| LOW | skills/research-lookup/scripts/research_lookup.py | 603 | CODE | |
| LOW | …ls/get-available-resources/scripts/detect_resources.py | 82 | CODE | |
| LOW | …ls/get-available-resources/scripts/detect_resources.py | 117 | CODE | |
| LOW | …ls/get-available-resources/scripts/detect_resources.py | 150 | CODE | |
| LOW | …ls/get-available-resources/scripts/detect_resources.py | 274 | CODE | |
| LOW | …ills/exploratory-data-analysis/scripts/eda_analyzer.py | 215 | CODE | |
| LOW | …ills/exploratory-data-analysis/scripts/eda_analyzer.py | 251 | CODE | |
| LOW | …ills/exploratory-data-analysis/scripts/eda_analyzer.py | 335 | CODE | |
| LOW | …ills/exploratory-data-analysis/scripts/eda_analyzer.py | 381 | CODE | |
| LOW | skills/iso-13485-certification/scripts/gap_analyzer.py | 197 | CODE | |
| LOW | …scientific-schematics/scripts/generate_schematic_ai.py | 214 | CODE | |
| LOW | …scientific-schematics/scripts/generate_schematic_ai.py | 321 | CODE | |
| LOW | …scientific-schematics/scripts/generate_schematic_ai.py | 399 | CODE | |
| LOW | skills/deeptools/scripts/validate_files.py | 46 | CODE | |
| LOW | skills/deeptools/scripts/workflow_generator.py | 422 | CODE | |
| LOW | skills/medchem/scripts/filter_molecules.py | 28 | CODE | |
| LOW | skills/pymatgen/scripts/structure_analyzer.py | 36 | CODE | |
| LOW | skills/pymatgen/scripts/structure_analyzer.py | 194 | CODE | |
| LOW | skills/pymatgen/scripts/structure_converter.py | 87 | CODE | |
| LOW | skills/pymatgen/scripts/phase_diagram_generator.py | 48 | CODE | |
| LOW | skills/citation-management/scripts/extract_metadata.py | 141 | CODE | |
| LOW | skills/citation-management/scripts/extract_metadata.py | 213 | CODE | |
| LOW | …s/citation-management/scripts/generate_schematic_ai.py | 214 | CODE | |
| LOW | …s/citation-management/scripts/generate_schematic_ai.py | 321 | CODE | |
| LOW | …s/citation-management/scripts/generate_schematic_ai.py | 399 | CODE | |
| LOW | skills/citation-management/scripts/format_bibtex.py | 201 | CODE | |
| LOW | skills/citation-management/scripts/format_bibtex.py | 213 | CODE | |
| LOW | …s/citation-management/scripts/search_google_scholar.py | 47 | CODE | |
| LOW | …ills/citation-management/scripts/validate_citations.py | 95 | CODE | |
| LOW | …ills/citation-management/scripts/validate_citations.py | 341 | CODE | |
| LOW | skills/citation-management/scripts/search_pubmed.py | 98 | CODE | |
| LOW | skills/citation-management/scripts/search_pubmed.py | 154 | CODE | |
| LOW | skills/pydicom/scripts/anonymize_dicom.py | 40 | CODE | |
| LOW | skills/pydicom/scripts/dicom_to_image.py | 52 | CODE | |
| LOW | skills/markitdown/scripts/generate_schematic_ai.py | 214 | CODE | |
| LOW | skills/markitdown/scripts/generate_schematic_ai.py | 321 | CODE | |
| LOW | skills/markitdown/scripts/generate_schematic_ai.py | 399 | CODE | |
| LOW | skills/xlsx/scripts/recalc.py | 73 | CODE | |
| LOW | skills/xlsx/scripts/office/pack.py | 24 | CODE | |
| LOW | skills/xlsx/scripts/office/pack.py | 108 | CODE | |
| LOW | skills/xlsx/scripts/office/validators/docx.py | 66 | CODE | |
| LOW | skills/xlsx/scripts/office/validators/docx.py | 112 | CODE | |
| LOW | skills/xlsx/scripts/office/validators/docx.py | 254 | CODE | |
| LOW | skills/xlsx/scripts/office/validators/docx.py | 298 | CODE | |
| LOW | skills/xlsx/scripts/office/validators/docx.py | 391 | CODE | |
| LOW | skills/xlsx/scripts/office/validators/redlining.py | 127 | CODE | |
| LOW | skills/xlsx/scripts/office/validators/redlining.py | 198 | CODE | |
| LOW | skills/xlsx/scripts/office/validators/pptx.py | 62 | CODE | |
| LOW | skills/xlsx/scripts/office/validators/pptx.py | 104 | CODE | |
| LOW | skills/xlsx/scripts/office/validators/pptx.py | 210 | CODE | |
| LOW | skills/xlsx/scripts/office/validators/base.py | 115 | CODE | |
| LOW | skills/xlsx/scripts/office/validators/base.py | 199 | CODE | |
| LOW | skills/xlsx/scripts/office/validators/base.py | 289 | CODE | |
| LOW | skills/xlsx/scripts/office/validators/base.py | 385 | CODE | |
| LOW | skills/xlsx/scripts/office/validators/base.py | 469 | CODE | |
| 169 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | scan_pr_skills.py | 15 | CODE | |
| LOW | tests/test_research_lookup.py | 3 | CODE | |
| LOW | skills/pymc/scripts/model_comparison.py | 22 | CODE | |
| LOW | skills/pymc/assets/hierarchical_model_template.py | 13 | CODE | |
| LOW | skills/pymc/assets/linear_regression_template.py | 13 | CODE | |
| LOW | skills/research-lookup/scripts/manuscript_packet.py | 3 | CODE | |
| LOW | skills/research-lookup/scripts/research_lookup.py | 9 | CODE | |
| LOW | skills/onekgpd/scripts/onekgpd_meta.py | 25 | CODE | |
| LOW | skills/onekgpd/scripts/onekgpd_api.py | 28 | CODE | |
| LOW | …ls/get-available-resources/scripts/detect_resources.py | 19 | CODE | |
| LOW | …ls/get-available-resources/scripts/detect_resources.py | 20 | CODE | |
| LOW | skills/experimental-design/scripts/doe_designs.py | 25 | CODE | |
| LOW | skills/experimental-design/scripts/randomization.py | 20 | CODE | |
| LOW | skills/iso-13485-certification/scripts/gap_analyzer.py | 16 | CODE | |
| LOW | skills/deeptools/scripts/validate_files.py | 12 | CODE | |
| LOW | skills/medchem/scripts/filter_molecules.py | 14 | CODE | |
| LOW | skills/pymatgen/scripts/structure_analyzer.py | 25 | CODE | |
| LOW | skills/pathway-enrichment/scripts/run_enrichment.py | 29 | CODE | |
| LOW | skills/citation-management/scripts/format_bibtex.py | 10 | CODE | |
| LOW | skills/markitdown/scripts/convert_literature.py | 14 | CODE | |
| LOW | skills/pytdc/scripts/load_and_split_data.py | 15 | CODE | |
| LOW | skills/xlsx/scripts/office/validators/__init__.py | 5 | CODE | |
| LOW | skills/xlsx/scripts/office/validators/__init__.py | 6 | CODE | |
| LOW | skills/xlsx/scripts/office/validators/__init__.py | 7 | CODE | |
| LOW | skills/xlsx/scripts/office/validators/__init__.py | 8 | CODE | |
| LOW | skills/exa-search/tests/test_exa_search.py | 12 | CODE | |
| LOW | skills/exa-search/scripts/exa_search.py | 16 | CODE | |
| LOW | skills/exa-search/scripts/exa_extract.py | 15 | CODE | |
| LOW | skills/autoskill/tests/test_e2e.py | 9 | CODE | |
| LOW | …ing/examples/covariates-forecasting/demo_covariates.py | 28 | CODE | |
| LOW | …casting/examples/anomaly-detection/detect_anomalies.py | 17 | CODE | |
| LOW | …orecasting/examples/global-temperature/run_forecast.py | 7 | CODE | |
| LOW | …recasting/examples/global-temperature/generate_html.py | 9 | CODE | |
| LOW | …ting/examples/global-temperature/visualize_forecast.py | 14 | CODE | |
| LOW | …examples/global-temperature/generate_animation_data.py | 11 | CODE | |
| LOW | …orecasting/examples/global-temperature/generate_gif.py | 8 | CODE | |
| LOW | skills/timesfm-forecasting/scripts/forecast_csv.py | 21 | CODE | |
| LOW | skills/timesfm-forecasting/scripts/check_system.py | 16 | CODE | |
| LOW | skills/arbor/scripts/tree.py | 34 | CODE | |
| LOW | …ills/statistical-analysis/scripts/assumption_checks.py | 16 | CODE | |
| LOW | …ills/statistical-analysis/scripts/assumption_checks.py | 17 | CODE | |
| LOW | …ical-decision-support/scripts/validate_cds_document.py | 19 | CODE | |
| LOW | …inical-decision-support/scripts/build_decision_tree.py | 12 | CODE | |
| LOW | skills/diffdock/scripts/analyze_results.py | 17 | CODE | |
| LOW | skills/diffdock/scripts/analyze_results.py | 19 | CODE | |
| LOW | skills/literature-review/scripts/verify_citations.py | 11 | CODE | |
| LOW | skills/scholar-evaluation/scripts/calculate_scores.py | 20 | CODE | |
| LOW | skills/pptx/scripts/office/validators/__init__.py | 5 | CODE | |
| LOW | skills/pptx/scripts/office/validators/__init__.py | 6 | CODE | |
| LOW | skills/pptx/scripts/office/validators/__init__.py | 7 | CODE | |
| LOW | skills/pptx/scripts/office/validators/__init__.py | 8 | CODE | |
| LOW | skills/primekg/scripts/query_primekg.py | 3 | CODE | |
| LOW | …ills/open-notebook/scripts/test_open_notebook_skill.py | 11 | CODE | |
| LOW | …et-research-reports/scripts/generate_market_visuals.py | 23 | CODE | |
| LOW | skills/deepchem/scripts/predict_solubility.py | 15 | CODE | |
| LOW | skills/scvelo/scripts/rna_velocity_workflow.py | 14 | CODE | |
| LOW | skills/scvelo/scripts/rna_velocity_workflow.py | 17 | CODE | |
| LOW | skills/simpy/scripts/resource_monitor.py | 11 | CODE | |
| LOW | skills/venue-templates/scripts/validate_format.py | 15 | CODE | |
| LOW | skills/venue-templates/scripts/query_template.py | 14 | CODE | |
| 42 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW⚡ | skills/deeptools/scripts/workflow_generator.py | 127 | # Step 2: Coverage assessment | COMMENT |
| LOW⚡ | skills/deeptools/scripts/workflow_generator.py | 135 | # Step 3: Fragment size (for paired-end data) | COMMENT |
| LOW⚡ | skills/deeptools/scripts/workflow_generator.py | 142 | # Step 4: ChIP signal strength | COMMENT |
| LOW⚡ | skills/deeptools/scripts/workflow_generator.py | 368 | # Step 2: Generate coverage track | COMMENT |
| LOW⚡ | skills/deeptools/scripts/workflow_generator.py | 378 | # Step 3: Fragment size analysis | COMMENT |
| LOW⚡ | skills/deeptools/scripts/workflow_generator.py | 385 | # Step 4: Compute matrix at peaks (if peaks provided) | COMMENT |
| LOW | skills/deeptools/scripts/workflow_generator.py | 106 | # Step 1: Correlation analysis | COMMENT |
| LOW | skills/deeptools/scripts/workflow_generator.py | 185 | # Step 1: Generate normalized coverage tracks | COMMENT |
| LOW | skills/deeptools/scripts/workflow_generator.py | 208 | # Step 2: Create log2 ratio track | COMMENT |
| LOW | skills/deeptools/scripts/workflow_generator.py | 221 | # Step 3: Compute matrix around TSS | COMMENT |
| LOW | skills/deeptools/scripts/workflow_generator.py | 235 | # Step 4: Generate heatmap | COMMENT |
| LOW | skills/deeptools/scripts/workflow_generator.py | 248 | # Step 5: Generate profile plot | COMMENT |
| LOW | skills/deeptools/scripts/workflow_generator.py | 260 | # Step 6: Enrichment at peaks (if peaks provided) | COMMENT |
| LOW | skills/deeptools/scripts/workflow_generator.py | 355 | # Step 1: Shift reads for Tn5 correction | COMMENT |
| LOW⚡ | …forecasting/examples/global-temperature/run_example.sh | 26 | # Step 1: Preflight check | COMMENT |
| LOW⚡ | …forecasting/examples/global-temperature/run_example.sh | 34 | # Step 2: Run forecast | COMMENT |
| LOW⚡ | …forecasting/examples/global-temperature/run_example.sh | 40 | # Step 3: Generate visualization | COMMENT |
| LOW⚡ | …ls/opentrons-integration/scripts/pcr_setup_template.py | 80 | # Step 1: Distribute master mix | COMMENT |
| LOW⚡ | …ls/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⚡ | skills/bioservices/scripts/compound_cross_reference.py | 337 | # Step 1: Search KEGG | STRING |
| LOW⚡ | skills/bioservices/scripts/compound_cross_reference.py | 343 | # Step 2: Get KEGG details | STRING |
| LOW⚡ | skills/bioservices/scripts/compound_cross_reference.py | 346 | # Step 3: Map to ChEMBL | STRING |
| LOW⚡ | skills/bioservices/scripts/compound_cross_reference.py | 349 | # Step 4: Get ChEBI details | STRING |
| LOW⚡ | skills/bioservices/scripts/compound_cross_reference.py | 354 | # Step 5: Get ChEMBL details | STRING |
| LOW⚡ | skills/bioservices/scripts/protein_analysis_workflow.py | 388 | # Step 1: Search protein | STRING |
| LOW⚡ | skills/bioservices/scripts/protein_analysis_workflow.py | 394 | # Step 2: Retrieve sequence | STRING |
| LOW⚡ | skills/bioservices/scripts/protein_analysis_workflow.py | 399 | # Step 3: BLAST search | STRING |
| LOW⚡ | skills/bioservices/scripts/protein_analysis_workflow.py | 404 | # Step 4: Pathway discovery | STRING |
| LOW⚡ | skills/bioservices/scripts/protein_analysis_workflow.py | 408 | # Step 5: Interaction mapping | STRING |
| LOW⚡ | skills/bioservices/scripts/protein_analysis_workflow.py | 411 | # Step 6: GO annotations | STRING |
| LOW | skills/gget/scripts/batch_sequence_analysis.py | 67 | # Step 1: BLAST each sequence | COMMENT |
| LOW⚡ | skills/gget/scripts/batch_sequence_analysis.py | 90 | # Step 2: Multiple sequence alignment | COMMENT |
| LOW⚡ | skills/gget/scripts/batch_sequence_analysis.py | 105 | # Step 3: Structure prediction (optional) | COMMENT |
| LOW⚡ | skills/gget/scripts/gene_analysis.py | 27 | # Step 1: Search for the gene | COMMENT |
| LOW⚡ | skills/gget/scripts/gene_analysis.py | 39 | # Step 2: Get detailed information | COMMENT |
| LOW | skills/gget/scripts/gene_analysis.py | 50 | # Step 3: Get sequences | COMMENT |
| LOW | skills/gget/scripts/gene_analysis.py | 63 | # Step 4: Get tissue expression | COMMENT |
| LOW⚡ | skills/gget/scripts/gene_analysis.py | 78 | # Step 5: Find correlated genes | COMMENT |
| LOW⚡ | skills/gget/scripts/gene_analysis.py | 92 | # Step 6: Get disease associations | COMMENT |
| LOW⚡ | skills/gget/scripts/gene_analysis.py | 105 | # Step 7: Get drug associations | COMMENT |
| LOW⚡ | …s/neuropixels-analysis/scripts/neuropixels_pipeline.py | 63 | # Step 1: High-pass filter | COMMENT |
| LOW⚡ | …s/neuropixels-analysis/scripts/neuropixels_pipeline.py | 67 | # Step 2: Detect bad channels | COMMENT |
| LOW⚡ | …s/neuropixels-analysis/scripts/neuropixels_pipeline.py | 75 | # Step 3: Phase shift (for Neuropixels 1.0) | COMMENT |
| LOW⚡ | …s/neuropixels-analysis/scripts/neuropixels_pipeline.py | 80 | # Step 4: Common median reference | COMMENT |
| LOW⚡ | skills/pymoo/scripts/decision_making_example.py | 138 | # Step 1: Run optimization | COMMENT |
| LOW⚡ | skills/pymoo/scripts/decision_making_example.py | 141 | # Step 2: Find extreme solutions | COMMENT |
| LOW⚡ | skills/pymoo/scripts/decision_making_example.py | 144 | # Step 3: Compare different preference weights | COMMENT |
| LOW⚡ | skills/pymoo/scripts/decision_making_example.py | 147 | # Step 4: Visualize selections with petal diagram | COMMENT |
| LOW⚡ | skills/phylogenetics/scripts/phylogenetic_analysis.py | 234 | # Step 1: Multiple Sequence Alignment | COMMENT |
| LOW⚡ | skills/phylogenetics/scripts/phylogenetic_analysis.py | 243 | # Step 2: Tree Inference | COMMENT |
| LOW | skills/phylogenetics/scripts/phylogenetic_analysis.py | 256 | # Step 3: Visualization | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| MEDIUM | skills/molfeat/SKILL.md | 161 | # MACCS - Fast, good for scaffold hopping | COMMENT |
| MEDIUM | skills/molfeat/SKILL.md | 216 | # MACCS - Fast, scaffold-based similarity | COMMENT |
| MEDIUM | skills/pytdc/scripts/load_and_split_data.py | 196 | # Example 1: Single prediction with scaffold split | COMMENT |
| MEDIUM | skills/nextflow/references/developing.md | 27 | │ └── mypipeline.nf # the primary workflow (orchestrates subworkflows) | CODE |
| MEDIUM | skills/nextflow/references/testing.md | 23 | nf-test init # creates nf-test.config + tests/ scaffolding in a project | CODE |
| MEDIUM | skills/nextflow/references/nf-core-tools.md | 120 | nf-core pipelines create # scaffold | CODE |
| MEDIUM | skills/timesfm-forecasting/SKILL.md | 337 | max_context=1024, # Max context window (truncates longer series) | CODE |
| MEDIUM⚡ | skills/datamol/SKILL.md | 278 | # Get Bemis-Murcko scaffold (core structure) | COMMENT |
| MEDIUM⚡ | skills/datamol/SKILL.md | 285 | # Group compounds by scaffold | COMMENT |
| MEDIUM⚡ | skills/datamol/SKILL.md | 291 | # Count scaffold frequency | COMMENT |
| MEDIUM⚡ | skills/datamol/SKILL.md | 295 | # Create scaffold-to-molecules mapping | COMMENT |
| MEDIUM | skills/datamol/SKILL.md | 560 | # Group by scaffold | COMMENT |
| MEDIUM | skills/datamol/SKILL.md | 571 | # Analyze each scaffold series | COMMENT |
| MEDIUM | skills/datamol/references/fragments_scaffolds.md | 3 | ## Scaffolds Module (`datamol.scaffold`) | COMMENT |
| MEDIUM⚡ | skills/datamol/references/fragments_scaffolds.md | 28 | # Count scaffold frequency | COMMENT |
| MEDIUM⚡ | skills/datamol/references/fragments_scaffolds.md | 36 | #### `dm.scaffold.fuzzy_scaffolding(mol, ...)` | COMMENT |
| MEDIUM⚡ | skills/datamol/references/fragments_scaffolds.md | 45 | # Group compounds by scaffold | COMMENT |
| MEDIUM | skills/datamol/references/fragments_scaffolds.md | 58 | # Group by scaffold and analyze activity | COMMENT |
| MEDIUM | skills/markdown-mermaid-writing/templates/kanban.md | 127 | | [Work item] | [Person] | [Person] | [#NNN](../../docs/project/pr/pr-00000001-agentic-docs-and-monorepo-modernization.m | CODE |
| MEDIUM | skills/markdown-mermaid-writing/templates/kanban.md | 138 | | [Work item] | [Person] | [Date] | [N days] | [#NNN](../../docs/project/pr/pr-00000001-agentic-docs-and-monorepo-m | CODE |
| MEDIUM | skills/markdown-mermaid-writing/templates/issue.md | 60 | | **Resolved in** | [PR-#NUMBER](../../docs/project/pr/pr-00000001-agentic-docs-and-monorepo-modernization.md) or | CODE |
| MEDIUM | skills/markdown-mermaid-writing/templates/issue.md | 163 | **Fixed in:** [PR-#NUMBER](../../docs/project/pr/pr-00000001-agentic-docs-and-monorepo-modernization.md) | CODE |
| MEDIUM | skills/markdown-mermaid-writing/templates/issue.md | 208 | | **Shipped in** | [PR-#NUMBER](../../docs/project/pr/pr-00000001-agentic-docs-and-monorepo-modernization.md) or N/A | CODE |
| MEDIUM | …lls/markdown-mermaid-writing/templates/pull_request.md | 49 | | **Related issues** | [#ISSUE](../../docs/project/issues/issue-00000001-agentic-documentation-system.md), [#ISSUE2](.. | CODE |
| MEDIUM | skills/rdkit/SKILL.md | 597 | # Generate Murcko scaffold hash | COMMENT |
| MEDIUM | skills/pufferlib/references/integration.md | 137 | # Create multi-agent environment | COMMENT |
| MEDIUM | skills/pufferlib/references/integration.md | 150 | # Train on multi-agent data | COMMENT |
| MEDIUM | skills/pufferlib/references/integration.md | 204 | # Large-scale multi-agent environment | COMMENT |
| MEDIUM | skills/optimize-for-gpu/references/cuvs.md | 422 | ### End-to-End RAG Pipeline Example | COMMENT |
| MEDIUM | skills/liteparse/references/output_formats.md | 141 | ## Layout-aware RAG patterns | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | skills/pymc/scripts/model_comparison.py | 104 | # Check if difference is significant relative to SE | COMMENT |
| LOW | …ls/get-available-resources/scripts/detect_resources.py | 156 | # Check if running on Apple Silicon | COMMENT |
| LOW | skills/iso-13485-certification/scripts/gap_analyzer.py | 207 | # Read file content (simple text reading) | COMMENT |
| LOW | skills/iso-13485-certification/scripts/gap_analyzer.py | 230 | # Check if any keyword appears in the document | COMMENT |
| LOW | …scientific-schematics/scripts/generate_schematic_ai.py | 678 | # Check if quality is acceptable - STOP EARLY if so | COMMENT |
| LOW | skills/deeptools/scripts/validate_files.py | 61 | # Check if start and end are integers | COMMENT |
| LOW | skills/deeptools/scripts/validate_files.py | 168 | # Check if any files were provided | STRING |
| LOW | skills/deeptools/scripts/validate_files.py | 180 | # Print results | STRING |
| LOW | skills/deeptools/scripts/workflow_generator.py | 478 | # Check if workflow was specified | STRING |
| LOW | skills/citation-management/scripts/extract_metadata.py | 46 | # Check if URL | COMMENT |
| LOW | …s/citation-management/scripts/generate_schematic_ai.py | 678 | # Check if quality is acceptable - STOP EARLY if so | COMMENT |
| LOW | skills/markitdown/scripts/generate_schematic_ai.py | 678 | # Check if quality is acceptable - STOP EARLY if so | COMMENT |
| LOW⚡ | skills/timesfm-forecasting/scripts/check_system.py | 388 | # Check if GPU is available | COMMENT |
| LOW | skills/infographics/scripts/generate_infographic_ai.py | 1142 | # Check if quality is acceptable | STRING |
| LOW | skills/pptx-posters/scripts/generate_schematic_ai.py | 678 | # Check if quality is acceptable - STOP EARLY if so | COMMENT |
| LOW | skills/treatment-plans/scripts/generate_schematic_ai.py | 678 | # Check if quality is acceptable - STOP EARLY if so | COMMENT |
| LOW⚡ | skills/treatment-plans/scripts/check_completeness.py | 295 | # Read file | STRING |
| LOW⚡ | skills/treatment-plans/scripts/check_completeness.py | 305 | # Display results | STRING |
| LOW | …lls/treatment-plans/scripts/validate_treatment_plan.py | 353 | # Display results | STRING |
| LOW⚡ | skills/treatment-plans/scripts/timeline_generator.py | 334 | # Check if any timeline info found | STRING |
| LOW | …ills/statistical-analysis/scripts/assumption_checks.py | 566 | # Check if grouped data | COMMENT |
| LOW | …ls/scientific-writing/scripts/generate_schematic_ai.py | 678 | # Check if quality is acceptable - STOP EARLY if so | COMMENT |
| LOW | …ical-decision-support/scripts/generate_schematic_ai.py | 678 | # Check if quality is acceptable - STOP EARLY if so | COMMENT |
| LOW | …ical-decision-support/scripts/validate_cds_document.py | 215 | # Check if gene appears but not in italics (\textit{} or \emph{}) | COMMENT |
| LOW | …nical-decision-support/scripts/create_cohort_tables.py | 47 | # Check if Fisher's exact is needed (expected count < 5) | COMMENT |
| LOW | skills/diffdock/scripts/analyze_results.py | 36 | # Check if this is a single complex or batch results | COMMENT |
| LOW | skills/diffdock/scripts/prepare_batch_csv.py | 130 | # Check if it's a file path or SMILES | COMMENT |
| LOW | skills/bioservices/scripts/protein_analysis_workflow.py | 76 | # Display results | COMMENT |
| LOW | …lls/literature-review/scripts/generate_schematic_ai.py | 678 | # Check if quality is acceptable - STOP EARLY if so | COMMENT |
| LOW⚡ | skills/literature-review/scripts/generate_pdf.py | 44 | # Check if pandoc is installed | COMMENT |
| LOW | …ls/scholar-evaluation/scripts/generate_schematic_ai.py | 678 | # Check if quality is acceptable - STOP EARLY if so | COMMENT |
| LOW | skills/deepchem/scripts/predict_solubility.py | 150 | # Display results | COMMENT |
| LOW | skills/latex-posters/scripts/generate_schematic_ai.py | 678 | # Check if quality is acceptable - STOP EARLY if so | COMMENT |
| LOW | skills/latex-posters/scripts/review_poster.sh | 13 | # Check if file argument provided | COMMENT |
| LOW | skills/latex-posters/scripts/review_poster.sh | 22 | # Check if file exists | COMMENT |
| LOW | skills/latex-posters/scripts/review_poster.sh | 93 | # Check if file is too large for email | COMMENT |
| LOW | skills/venue-templates/scripts/generate_schematic_ai.py | 678 | # Check if quality is acceptable - STOP EARLY if so | COMMENT |
| LOW | skills/venue-templates/scripts/validate_format.py | 175 | # Print results | COMMENT |
| LOW | …ills/clinical-reports/scripts/generate_schematic_ai.py | 678 | # Check if quality is acceptable - STOP EARLY if so | COMMENT |
| LOW | …lls/scientific-slides/scripts/validate_presentation.py | 387 | # Print results | STRING |
| LOW | …lls/scientific-slides/scripts/generate_schematic_ai.py | 678 | # Check if quality is acceptable - STOP EARLY if so | COMMENT |
| LOW | …hypothesis-generation/scripts/generate_schematic_ai.py | 678 | # Check if quality is acceptable - STOP EARLY if so | COMMENT |
| LOW | skills/rdkit/scripts/similarity_search.py | 288 | # Output results | STRING |
| LOW | skills/rdkit/scripts/molecular_properties.py | 131 | # Output results | COMMENT |
| LOW | skills/stable-baselines3/scripts/custom_env_template.py | 135 | # Check if goal is reached | COMMENT |
| LOW | skills/pufferlib/scripts/env_template.py | 102 | # Check if episode is done | COMMENT |
| LOW | skills/pymoo/scripts/many_objective_example.py | 44 | # Print results summary | COMMENT |
| LOW | skills/pymoo/scripts/single_objective_example.py | 45 | # Print results | COMMENT |
| LOW | skills/pymoo/scripts/multi_objective_example.py | 36 | # Print results summary | COMMENT |
| LOW | skills/labarchive-integration/scripts/setup_config.py | 167 | # Check if config already exists | COMMENT |
| LOW | skills/peer-review/scripts/generate_schematic_ai.py | 678 | # Check if quality is acceptable - STOP EARLY if so | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| MEDIUM | skills/iso-13485-certification/scripts/gap_analyzer.py | 249 | """Generate comprehensive gap analysis report.""" | STRING |
| MEDIUM | …scientific-schematics/scripts/generate_schematic_ai.py | 74 | # Scientific diagram best practices prompt template | COMMENT |
| MEDIUM | …s/citation-management/scripts/generate_schematic_ai.py | 74 | # Scientific diagram best practices prompt template | COMMENT |
| MEDIUM | skills/markitdown/scripts/generate_schematic_ai.py | 74 | # Scientific diagram best practices prompt template | COMMENT |
| MEDIUM | skills/pptx-posters/scripts/generate_schematic_ai.py | 74 | # Scientific diagram best practices prompt template | COMMENT |
| MEDIUM | skills/treatment-plans/scripts/generate_schematic_ai.py | 74 | # Scientific diagram best practices prompt template | COMMENT |
| MEDIUM | …lls/treatment-plans/scripts/validate_treatment_plan.py | 178 | """Display comprehensive validation results.""" | STRING |
| MEDIUM | …ills/statistical-analysis/scripts/assumption_checks.py | 186 | # Levene's test (robust to non-normality) | COMMENT |
| MEDIUM | …ills/statistical-analysis/scripts/assumption_checks.py | 646 | # Run comprehensive check | COMMENT |
| MEDIUM | …ls/scientific-writing/scripts/generate_schematic_ai.py | 74 | # Scientific diagram best practices prompt template | COMMENT |
| MEDIUM | …ical-decision-support/scripts/generate_schematic_ai.py | 74 | # Scientific diagram best practices prompt template | COMMENT |
| MEDIUM | …lls/literature-review/scripts/generate_schematic_ai.py | 74 | # Scientific diagram best practices prompt template | COMMENT |
| MEDIUM | …ls/scholar-evaluation/scripts/generate_schematic_ai.py | 74 | # Scientific diagram best practices prompt template | COMMENT |
| MEDIUM | skills/scholar-evaluation/scripts/calculate_scores.py | 149 | """Generate comprehensive evaluation report.""" | STRING |
| MEDIUM | …et-research-reports/scripts/generate_market_visuals.py | 15 | # Generate all 28 visuals (for comprehensive coverage) | STRING |
| MEDIUM | skills/latex-posters/scripts/generate_schematic_ai.py | 74 | # Scientific diagram best practices prompt template | COMMENT |
| MEDIUM | skills/pyopenms/scripts/accurate_mass_search.py | 94 | # Re-read the mzTab text for a robust flat dump of the SML table | COMMENT |
| MEDIUM | skills/matplotlib/scripts/plot_template.py | 322 | """Create a comprehensive figure with multiple subplots.""" | STRING |
| MEDIUM | skills/venue-templates/scripts/generate_schematic_ai.py | 74 | # Scientific diagram best practices prompt template | COMMENT |
| MEDIUM | …ills/clinical-reports/scripts/generate_schematic_ai.py | 74 | # Scientific diagram best practices prompt template | COMMENT |
| MEDIUM | skills/clinical-reports/scripts/validate_case_report.py | 192 | """Generate comprehensive validation report.""" | STRING |
| MEDIUM | …lls/scientific-slides/scripts/generate_schematic_ai.py | 74 | # Scientific diagram best practices prompt template | COMMENT |
| MEDIUM | …hypothesis-generation/scripts/generate_schematic_ai.py | 74 | # Scientific diagram best practices prompt template | COMMENT |
| MEDIUM | skills/rdkit/scripts/molecular_properties.py | 26 | """Calculate comprehensive molecular properties.""" | STRING |
| MEDIUM | skills/peer-review/scripts/generate_schematic_ai.py | 74 | # Scientific diagram best practices prompt template | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | skills/anndata/references/best_practices.md | 261 | gene_expr = adata.raw[:, 'GENE_NAME'].X | COMMENT |
| LOW | skills/exploratory-data-analysis/SKILL.md | 301 | df = pd.read_csv('experiment_results.csv') | COMMENT |
| LOW | skills/exploratory-data-analysis/SKILL.md | 321 | # 2. Read reference for ND2 format | COMMENT |
| LOW | skills/bids/references/conversion_tools.md | 361 | #### Step 4: Convert | COMMENT |
| LOW | skills/bids/references/beps.yml | 1 | --- | COMMENT |
| LOW | skills/pymatgen/references/transformations_workflows.md | 301 | relax = MPRelaxSet(slab) | COMMENT |
| LOW | skills/markitdown/SKILL.md | 181 | COMMENT | |
| LOW | skills/autoskill/config.yaml | 1 | # autoskill configuration | COMMENT |
| LOW | skills/autoskill/references/screenpipe-config.yaml | 1 | # Starter screenpipe configuration for autoskill users. | COMMENT |
| LOW | …forecasting/examples/global-temperature/run_example.sh | 1 | #!/bin/bash | COMMENT |
| LOW | …nical-decision-support/scripts/biomarker_classifier.py | 381 | # PT001,55.5,12.3,1+,Yes,14.2,1 | COMMENT |
| LOW | …inical-decision-support/scripts/build_decision_tree.py | 441 | # Example usage: | COMMENT |
| LOW | …nical-decision-support/scripts/create_cohort_tables.py | 521 | # PT001,Biomarker+,65,Male,0-1,IV,PR,1,0,... | COMMENT |
| LOW | skills/diffdock/assets/custom_inference_config.yaml | 61 | # samples_per_complex: 30 | COMMENT |
| LOW | skills/diffdock/assets/custom_inference_config.yaml | 81 | # PRESET 4: Rigid Ligands (more focused predictions) | COMMENT |
| LOW | skills/gget/references/workflows.md | 561 | mut["pdb_id"] = None | COMMENT |
| LOW | skills/literature-review/SKILL.md | 561 | --summary | COMMENT |
| LOW | …ls/literature-review/references/database_strategies.md | 421 | # 2. Search bioRxiv | COMMENT |
| LOW | skills/latex-posters/SKILL.md | 481 | python scripts/generate_schematic.py "POSTER FORMAT for A0. ONE case: Company logo + 'FDA APPROVED' (150pt bold) + '2024 | COMMENT |
| LOW | skills/pytorch-lightning/scripts/template_datamodule.py | 321 | print(f"Train batches: {len(train_loader)}") | COMMENT |
| LOW | skills/stable-baselines3/scripts/evaluate_agent.py | 201 | # Example 1: Evaluate a trained model | COMMENT |
| LOW | skills/stable-baselines3/scripts/evaluate_agent.py | 221 | # watch_agent( | COMMENT |
| LOW | skills/stable-baselines3/scripts/evaluate_agent.py | 241 | # model_path="./models/best_model/best_model.zip", | COMMENT |
| LOW | skills/stable-baselines3/scripts/train_rl_agent.py | 141 | algorithm=PPO, | COMMENT |
| LOW | skills/stable-baselines3/scripts/train_rl_agent.py | 161 | # algorithm=DQN, | COMMENT |
| LOW | skills/stable-baselines3/scripts/custom_env_template.py | 61 | # 2. Multi-discrete: spaces.MultiDiscrete([n1, n2, ...]) | COMMENT |
| LOW | skills/pufferlib/scripts/env_template.py | 41 | # 'position': (2,), | COMMENT |
| LOW | skills/optimize-for-gpu/SKILL.md | 261 | # Warp (simulation, spatial computing, differentiable programming) | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | skills/pymc/scripts/model_comparison.py | 360 | # Example usage | STRING |
| LOW | skills/pymc/scripts/model_diagnostics.py | 323 | # Example usage | COMMENT |
| LOW | …forecasting/examples/global-temperature/run_example.sh | 9 | # Usage: | COMMENT |
| LOW | …ills/statistical-analysis/scripts/assumption_checks.py | 634 | # Example usage | COMMENT |
| LOW | …decision-support/scripts/generate_survival_analysis.py | 413 | # Example usage: | COMMENT |
| LOW | …ical-decision-support/scripts/validate_cds_document.py | 331 | # Example usage: | COMMENT |
| LOW | …nical-decision-support/scripts/biomarker_classifier.py | 375 | # Example usage: | COMMENT |
| LOW | …inical-decision-support/scripts/build_decision_tree.py | 441 | # Example usage: | COMMENT |
| LOW | …nical-decision-support/scripts/create_cohort_tables.py | 515 | # Example usage: | COMMENT |
| LOW | skills/simpy/scripts/resource_monitor.py | 320 | # Example usage | COMMENT |
| LOW | skills/pytorch-lightning/scripts/template_datamodule.py | 301 | # Example usage | COMMENT |
| LOW | …pytorch-lightning/scripts/template_lightning_module.py | 198 | # Example usage | COMMENT |
| LOW⚡ | …ills/scientific-visualization/scripts/figure_export.py | 318 | # Example usage | COMMENT |
| LOW | skills/scikit-learn/scripts/clustering_analysis.py | 338 | # Example usage | COMMENT |
| LOW | skills/scikit-learn/scripts/classification_pipeline.py | 230 | # Example usage | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| MEDIUM | skills/open-notebook/scripts/chat_interaction.py | 140 | # Create a notebook with some content first | COMMENT |
| MEDIUM | skills/open-notebook/scripts/chat_interaction.py | 162 | # Create a chat session | COMMENT |
| MEDIUM | skills/open-notebook/scripts/source_ingestion.py | 124 | # Create a notebook first | COMMENT |
| MEDIUM | skills/hypogenic/references/config_template.yaml | 116 | # Define a custom function in your code to parse specific output formats | COMMENT |
| MEDIUM | skills/pymoo/scripts/many_objective_example.py | 19 | # Define the problem - DTLZ2 with 5 objectives | COMMENT |
| MEDIUM | skills/pymoo/scripts/single_objective_example.py | 21 | # Define the problem - Sphere function (sum of squares) | COMMENT |
| MEDIUM | skills/pymoo/scripts/multi_objective_example.py | 18 | # Define the problem - ZDT1 (bi-objective) | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | skills/xlsx/scripts/office/validators/__init__.py | 10 | __all__ = [ | CODE |
| LOW | skills/pptx/scripts/clean.py | 221 | def update_content_types(unpacked_dir: Path, removed_files: list[str]) -> None: | CODE |
| LOW | skills/pptx/scripts/office/validators/__init__.py | 10 | __all__ = [ | CODE |
| LOW | …ills/scientific-visualization/scripts/style_presets.py | 195 | def set_color_palette(palette_name: str = 'okabe_ito') -> None: | CODE |
| LOW | skills/docx/scripts/accept_changes.py | 14 | logger = logging.getLogger(__name__) | CODE |
| LOW | skills/docx/scripts/office/validators/__init__.py | 10 | __all__ = [ | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | skills/research-lookup/scripts/research_lookup.py | 143 | CODE | |
| LOW | skills/infographics/scripts/generate_infographic_ai.py | 991 | CODE | |
| LOW | …nical-decision-support/scripts/create_cohort_tables.py | 419 | CODE | |
| LOW | …s/neuropixels-analysis/scripts/preprocess_recording.py | 15 | CODE | |
| LOW | skills/stable-baselines3/scripts/train_rl_agent.py | 24 | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | skills/pptx-posters/assets/poster_html_template.html | 206 | <div id="chart1" class="placeholder" style="width: 100%; height: 400pt;"></div> | CODE |
| LOW | skills/pptx-posters/assets/poster_quality_checklist.md | 15 | - [ ] No placeholder text remaining (TODO, Lorem ipsum, etc.) | CODE |
| LOW | skills/latex-posters/SKILL.md | 1070 | - [ ] No placeholder text remaining (Lorem ipsum, TODO, etc.) | CODE |
| LOW | skills/latex-posters/scripts/review_poster.sh | 179 | echo " [ ] No placeholder text (Lorem ipsum, TODO, etc.)" | CODE |
| LOW | skills/latex-posters/assets/poster_quality_checklist.md | 15 | - [ ] No placeholder text remaining (TODO, Lorem ipsum, etc.) | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| HIGH | skills/latex-posters/SKILL.md | 114 | The #1 issue with AI-generated poster graphics is **TOO MUCH CONTENT**. This causes: | CODE |