Repository Analysis

K-Dense-AI/scientific-agent-skills

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.

11.6 Low AI signal View on GitHub

Analysis Overview

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).

11.6
Adjusted Score
11.6
Raw Score
100%
Time Factor
2026-07-14
Last Push
30.9K
Stars
Python
Language
479.9K
Lines of Code
1.3K
Files
2.7K
Pattern Hits
2026-07-14
Scan Date
0.32
HC Hit Rate

What These Metrics Mean

Adjusted Score
Primary synthetic code indicator. Raw score normalised per 1,000 lines of code and multiplied by the temporal discount factor. This is the definitive comparative metric — use it to rank repositories by AI authorship density.
Raw Score
The unmodified sum of all severity-weighted, context-multiplied pattern match scores before temporal discounting. Reflects the absolute signal strength independent of when the repository was last active.
Time Factor
The temporal discount multiplier (0–100%) applied to the raw score. Repositories last updated before ChatGPT's launch (Nov 2022) receive a 5% factor. Full signal is only assigned to repositories active in the post-adoption era (Jan 2024+).
Pattern Hits
Total count of individual pattern matches across all files and categories. A high hit count with a low score may indicate a very large codebase with isolated AI snippets; a low count with a high score indicates dense, concentrated AI signatures.
HC Hit Rate
High+Critical pattern hits per file, averaged across the repository. This orthogonal signal catches repositories where a few files are densely packed with high-severity AI tells — a strong indicator even when the normalised score appears moderate due to codebase size.
Lines of Code / Files
Total lines and files analysed. The scanner examines 94 file extensions. These denominators are used to normalise the score, enabling fair comparison between repositories of vastly different sizes.

Score History

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.

Severity Breakdown

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.

CRITICAL 0HIGH 417MEDIUM 564LOW 1732

Directory Score Breakdown

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.

Pattern Findings

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.

Cross-File Repetition303 hits · 1515 pts
SeverityFileLineSnippetContext
HIGH…scientific-schematics/scripts/generate_schematic_ai.py0ai-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.py0ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: STRING
HIGHskills/markitdown/scripts/generate_schematic_ai.py0ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: STRING
HIGHskills/pptx-posters/scripts/generate_schematic_ai.py0ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: STRING
HIGHskills/treatment-plans/scripts/generate_schematic_ai.py0ai-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.py0ai-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.py0ai-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.py0ai-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.py0ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: STRING
HIGHskills/latex-posters/scripts/generate_schematic_ai.py0ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: STRING
HIGHskills/venue-templates/scripts/generate_schematic_ai.py0ai-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.py0ai-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.py0ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: STRING
HIGH…hypothesis-generation/scripts/generate_schematic_ai.py0ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: STRING
HIGHskills/peer-review/scripts/generate_schematic_ai.py0ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: STRING
HIGH…scientific-schematics/scripts/generate_schematic_ai.py0load .env file from current directory or script directory only.STRING
HIGH…s/citation-management/scripts/generate_schematic_ai.py0load .env file from current directory or script directory only.STRING
HIGHskills/markitdown/scripts/generate_schematic_ai.py0load .env file from current directory or script directory only.STRING
HIGHskills/infographics/scripts/generate_infographic_ai.py0load .env file from current directory or script directory only.STRING
HIGHskills/pptx-posters/scripts/generate_schematic_ai.py0load .env file from current directory or script directory only.STRING
HIGHskills/treatment-plans/scripts/generate_schematic_ai.py0load .env file from current directory or script directory only.STRING
HIGH…ls/scientific-writing/scripts/generate_schematic_ai.py0load .env file from current directory or script directory only.STRING
HIGH…ical-decision-support/scripts/generate_schematic_ai.py0load .env file from current directory or script directory only.STRING
HIGH…lls/literature-review/scripts/generate_schematic_ai.py0load .env file from current directory or script directory only.STRING
HIGH…ls/scholar-evaluation/scripts/generate_schematic_ai.py0load .env file from current directory or script directory only.STRING
HIGHskills/latex-posters/scripts/generate_schematic_ai.py0load .env file from current directory or script directory only.STRING
HIGHskills/venue-templates/scripts/generate_schematic_ai.py0load .env file from current directory or script directory only.STRING
HIGH…ills/clinical-reports/scripts/generate_schematic_ai.py0load .env file from current directory or script directory only.STRING
HIGH…lls/scientific-slides/scripts/generate_schematic_ai.py0load .env file from current directory or script directory only.STRING
HIGH…s/scientific-slides/scripts/generate_slide_image_ai.py0load .env file from current directory or script directory only.STRING
HIGH…hypothesis-generation/scripts/generate_schematic_ai.py0load .env file from current directory or script directory only.STRING
HIGHskills/peer-review/scripts/generate_schematic_ai.py0load .env file from current directory or script directory only.STRING
HIGH…scientific-schematics/scripts/generate_schematic_ai.py0generate 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.py0generate scientific schematics using ai with smart iterative refinement. uses gemini 3.1 pro preview for quality review STRING
HIGHskills/markitdown/scripts/generate_schematic_ai.py0generate scientific schematics using ai with smart iterative refinement. uses gemini 3.1 pro preview for quality review STRING
HIGHskills/pptx-posters/scripts/generate_schematic_ai.py0generate scientific schematics using ai with smart iterative refinement. uses gemini 3.1 pro preview for quality review STRING
HIGHskills/treatment-plans/scripts/generate_schematic_ai.py0generate 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.py0generate 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.py0generate 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.py0generate 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.py0generate scientific schematics using ai with smart iterative refinement. uses gemini 3.1 pro preview for quality review STRING
HIGHskills/latex-posters/scripts/generate_schematic_ai.py0generate scientific schematics using ai with smart iterative refinement. uses gemini 3.1 pro preview for quality review STRING
HIGHskills/venue-templates/scripts/generate_schematic_ai.py0generate 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.py0generate 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.py0generate 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.py0generate scientific schematics using ai with smart iterative refinement. uses gemini 3.1 pro preview for quality review STRING
HIGHskills/peer-review/scripts/generate_schematic_ai.py0generate 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.py0create 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.py0create a high-quality scientific diagram with these requirements: visual quality: - clean white or light background (no STRING
HIGHskills/markitdown/scripts/generate_schematic_ai.py0create a high-quality scientific diagram with these requirements: visual quality: - clean white or light background (no STRING
HIGHskills/pptx-posters/scripts/generate_schematic_ai.py0create a high-quality scientific diagram with these requirements: visual quality: - clean white or light background (no STRING
HIGHskills/treatment-plans/scripts/generate_schematic_ai.py0create 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.py0create 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.py0create 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.py0create 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.py0create a high-quality scientific diagram with these requirements: visual quality: - clean white or light background (no STRING
HIGHskills/latex-posters/scripts/generate_schematic_ai.py0create a high-quality scientific diagram with these requirements: visual quality: - clean white or light background (no STRING
HIGHskills/venue-templates/scripts/generate_schematic_ai.py0create 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.py0create 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.py0create a high-quality scientific diagram with these requirements: visual quality: - clean white or light background (no STRING
243 more matches not shown…
Excessive Try-Catch Wrapping672 hits · 945 pts
SeverityFileLineSnippetContext
LOWscan_pr_skills.py63 except Exception as exc: # pragma: no cover - defensiveCODE
LOWscan_pr_skills.py84 except Exception as exc: # pragma: no cover - defensiveCODE
LOWscan_skills.py174 except Exception as e:CODE
LOWscan_skills.py198 except Exception as e:CODE
LOW…lls/benchling-integration/references/authentication.md328except Exception as e:CODE
MEDIUMskills/networkx/references/io.md447 print(f"Error reading GraphML: {e}")CODE
LOWskills/research-lookup/scripts/research_lookup.py936 except Exception as exc:CODE
LOWskills/research-lookup/scripts/research_lookup.py951 except Exception as fallback_exc:CODE
LOWskills/research-lookup/scripts/research_lookup.py1167 except Exception as exc:STRING
MEDIUMskills/research-lookup/scripts/research_lookup.py1168 print(f"Error: {exc}", file=sys.stderr)STRING
MEDIUMskills/shap/references/workflows.md70print(f"Error rate: {len(error_indices) / len(y_test):.2%}")CODE
LOWskills/dask/references/futures.md499 except Exception as e:CODE
LOWskills/dask/references/futures.md533except Exception:CODE
LOW…ls/get-available-resources/scripts/detect_resources.py40 except Exception:CODE
LOW…ls/get-available-resources/scripts/detect_resources.py75 except Exception as e:CODE
LOW…ls/get-available-resources/scripts/detect_resources.py195 except Exception:CODE
LOW…ls/get-available-resources/scripts/detect_resources.py199 except Exception:CODE
LOW…ills/exploratory-data-analysis/scripts/eda_analyzer.py209 except Exception as e:CODE
MEDIUM…ills/exploratory-data-analysis/scripts/eda_analyzer.py210 print(f"Error loading reference: {e}", file=sys.stderr)CODE
LOW…ills/exploratory-data-analysis/scripts/eda_analyzer.py245 except Exception as e:CODE
LOW…ills/exploratory-data-analysis/scripts/eda_analyzer.py329 except Exception as e:CODE
LOW…ills/exploratory-data-analysis/scripts/eda_analyzer.py375 except Exception as e:CODE
LOW…ills/exploratory-data-analysis/scripts/eda_analyzer.py415 except Exception as e:CODE
MEDIUM…ills/exploratory-data-analysis/scripts/eda_analyzer.py529 print(f"Error: File not found: {filepath}")CODE
LOWskills/iso-13485-certification/scripts/gap_analyzer.py217 except Exception as e:CODE
LOWskills/esm/references/forge-api.md363 except Exception as e:CODE
MEDIUMskills/esm/references/forge-api.md364 print(f"Error processing {i}: {e}")CODE
LOWskills/esm/references/forge-api.md404 except Exception as e:CODE
LOWskills/esm/references/forge-api.md582 except Exception as e:CODE
LOWskills/esm/references/forge-api.md641except Exception as e:CODE
MEDIUM…scientific-schematics/scripts/generate_schematic_ai.py33 print("Error: requests library not found. Install with: pip install requests")CODE
LOW…scientific-schematics/scripts/generate_schematic_ai.py288 except Exception as e:CODE
LOW…scientific-schematics/scripts/generate_schematic_ai.py391 except Exception as e:CODE
LOW…scientific-schematics/scripts/generate_schematic_ai.py548 except Exception as e:CODE
MEDIUM…scientific-schematics/scripts/generate_schematic_ai.py782 print("Error: OPENROUTER_API_KEY environment variable not set")STRING
MEDIUM…scientific-schematics/scripts/generate_schematic_ai.py790 print("Error: Iterations must be between 1 and 2")STRING
LOW…scientific-schematics/scripts/generate_schematic_ai.py810 except Exception as e:STRING
MEDIUM…ls/scientific-schematics/scripts/generate_schematic.py95 print("Error: OPENROUTER_API_KEY environment variable not set")STRING
MEDIUM…ls/scientific-schematics/scripts/generate_schematic.py108 print(f"Error: AI generation script not found: {ai_script}")STRING
LOW…ls/scientific-schematics/scripts/generate_schematic.py132 except Exception as e:STRING
MEDIUM…ls/scientific-schematics/scripts/generate_schematic.py133 print(f"Error executing AI generation: {e}")STRING
LOWskills/pyzotero/references/files-attachments.md95 except Exception as e:CODE
LOWskills/pyzotero/references/error-handling.md45except Exception as e:CODE
LOWskills/pyzotero/references/error-handling.md105except Exception as e:CODE
LOWskills/deeptools/scripts/validate_files.py72 except Exception as e:CODE
MEDIUMskills/medchem/scripts/filter_molecules.py23 print(f"Error: Missing required package: {e}")CODE
MEDIUMskills/medchem/scripts/filter_molecules.py50 print(f"Error: Column '{smiles_column}' not found")CODE
MEDIUMskills/medchem/scripts/filter_molecules.py65 print(f"Error: Unsupported file format: {suffix}")CODE
MEDIUMskills/medchem/scripts/filter_molecules.py237 print("Error: Specify at least one filter (--rules, --query, --pains, --nibr, etc.)")CODE
LOWskills/fluidsim/references/advanced_features.md257 except Exception as e:STRING
MEDIUMskills/fluidsim/references/advanced_features.md258 print(f"Error loading {sim_dir}: {e}")STRING
LOWskills/pymatgen/references/materials_project_api.md432except Exception as e:CODE
MEDIUMskills/pymatgen/scripts/structure_analyzer.py32 print("Error: pymatgen is not installed. Install with: pip install pymatgen")CODE
LOWskills/pymatgen/scripts/structure_analyzer.py125 except Exception as e:CODE
LOWskills/pymatgen/scripts/structure_analyzer.py165 except Exception as e:CODE
LOWskills/pymatgen/scripts/structure_analyzer.py239 except Exception as e:CODE
MEDIUMskills/pymatgen/scripts/structure_analyzer.py240 print(f"Error reading structure file: {e}")CODE
MEDIUMskills/pymatgen/scripts/structure_analyzer.py262 print("Error: PyYAML is not installed. Install with: pip install pyyaml")CODE
MEDIUMskills/pymatgen/scripts/structure_converter.py27 print("Error: pymatgen is not installed. Install with: pip install pymatgen")CODE
MEDIUMskills/pymatgen/scripts/structure_converter.py52 print("Error: Must specify either output_path or output_format")CODE
612 more matches not shown…
Structural Annotation Overuse527 hits · 876 pts
SeverityFileLineSnippetContext
LOWskills/qiskit/references/patterns.md27## Step 1: MapCOMMENT
LOWskills/qiskit/references/patterns.md116## Step 2: OptimizeCOMMENT
LOWskills/qiskit/references/patterns.md163## Step 3: ExecuteCOMMENT
LOWskills/qiskit/references/patterns.md259## Step 4: Post-processCOMMENT
LOWskills/shap/SKILL.md39### Step 1: Select the Right ExplainerCOMMENT
LOWskills/shap/SKILL.md60### Step 2: Compute SHAP ValuesCOMMENT
LOWskills/shap/SKILL.md83### Step 3: Visualize ResultsCOMMENT
LOWskills/shap/SKILL.md135# Step 3: Global importanceCOMMENT
LOWskills/shap/SKILL.md138# Step 4: Feature relationshipsCOMMENT
LOWskills/shap/SKILL.md141# Step 5: Individual explanationCOMMENT
LOWskills/shap/references/workflows.md24# Step 1: Load and split dataCOMMENT
LOWskills/shap/references/workflows.md27# Step 2: Train model (example with XGBoost)COMMENT
LOWskills/shap/references/workflows.md32# Step 3: Create explainerCOMMENT
LOWskills/shap/references/workflows.md35# Step 4: Compute SHAP valuesCOMMENT
LOWskills/shap/references/workflows.md38# Step 5: Visualize global importanceCOMMENT
LOWskills/shap/references/workflows.md41# Step 6: Examine top features in detailCOMMENT
LOWskills/shap/references/workflows.md45# Step 7: Explain individual predictionsCOMMENT
LOWskills/shap/references/workflows.md59# Step 1: Compute SHAP valuesCOMMENT
LOWskills/shap/references/workflows.md63# Step 2: Identify prediction errorsCOMMENT
LOWskills/shap/references/workflows.md68# Step 3: Analyze errorsCOMMENT
LOWskills/shap/references/workflows.md72# Step 4: Explain misclassified samplesCOMMENT
LOWskills/shap/references/workflows.md78# Step 5: Check if model learned correct patternsCOMMENT
LOWskills/shap/references/workflows.md82# Step 6: Investigate specific feature relationshipsCOMMENT
LOWskills/shap/references/workflows.md88# Step 7: Validate feature interactionsCOMMENT
LOWskills/shap/references/workflows.md120# Step 3: Engineer new features based on insightsCOMMENT
LOWskills/shap/references/workflows.md125# Step 4: Retrain with engineered featuresCOMMENT
LOWskills/shap/references/workflows.md130# Step 5: Compare feature importanceCOMMENT
LOWskills/shap/references/workflows.md136# Step 6: Validate improvementCOMMENT
LOWskills/shap/references/workflows.md156# Step 1: Train multiple modelsCOMMENT
LOWskills/shap/references/workflows.md163# Step 2: Compute SHAP values for each modelCOMMENT
LOWskills/shap/references/workflows.md172# Step 3: Compare global feature importanceCOMMENT
LOWskills/shap/references/workflows.md175# Step 4: Compare model scoresCOMMENT
LOWskills/shap/references/workflows.md180# Step 5: Check consistency of feature importanceCOMMENT
LOWskills/shap/references/workflows.md190# Step 6: Analyze specific predictions across modelsCOMMENT
LOWskills/shap/references/workflows.md196# Step 7: Decision based on:COMMENT
LOWskills/shap/references/workflows.md214# Step 1: Identify protected attributesCOMMENT
LOWskills/shap/references/workflows.md217# Step 2: Compute SHAP valuesCOMMENT
LOWskills/shap/references/workflows.md221# Step 3: Compare feature importance across groupsCOMMENT
LOWskills/shap/references/workflows.md229# Step 4: Check if protected attribute has high SHAP importanceCOMMENT
LOWskills/shap/references/workflows.md234# Step 5: Analyze predictions for each groupCOMMENT
LOWskills/shap/references/workflows.md276# Step 1: Load or build neural networkCOMMENT
LOWskills/shap/references/workflows.md279# Step 2: Select background datasetCOMMENT
LOWskills/shap/references/workflows.md283# Step 3: Create DeepExplainerCOMMENT
LOWskills/shap/references/workflows.md286# Step 4: Compute SHAP values (may take time)COMMENT
LOWskills/shap/references/workflows.md291# Step 5: Handle multi-output modelsCOMMENT
LOWskills/shap/references/workflows.md332# Step 1: Train and save modelCOMMENT
LOWskills/shap/references/workflows.md336# Step 2: Create and save explainerCOMMENT
LOWskills/shap/references/workflows.md340# Step 3: Create explanation serviceCOMMENT
LOWskills/shap/references/workflows.md433# Step 1: Prepare data with time-based featuresCOMMENT
LOWskills/shap/references/workflows.md441# Step 2: Train modelCOMMENT
LOWskills/shap/references/workflows.md446# Step 3: Compute SHAP valuesCOMMENT
LOWskills/shap/references/workflows.md450# Step 4: Analyze temporal patternsCOMMENT
LOWskills/shap/references/workflows.md454# Step 5: Check lagged feature importanceCOMMENT
LOWskills/shap/references/workflows.md460# Step 6: Explain specific predictionsCOMMENT
LOWskills/shap/references/workflows.md465# Step 7: Validate seasonality understandingCOMMENT
LOWskills/shap/references/workflows.md104# Step 1: Initial model with baseline featuresCOMMENT
LOWskills/shap/references/workflows.md109# Step 2: Identify feature engineering opportunitiesCOMMENT
LOWskills/shap/references/workflows.md246# Step 6: Check for proxy featuresCOMMENT
LOWskills/shap/references/workflows.md255# Step 7: Mitigation strategies if bias foundCOMMENT
LOWskills/shap/references/workflows.md309# Step 6: VisualizeCOMMENT
467 more matches not shown…
Decorative Section Separators178 hits · 538 pts
SeverityFileLineSnippetContext
MEDIUMskills/pymc/references/workflows.md16# ===============COMMENT
MEDIUMskills/pymc/references/workflows.md24# ==============COMMENT
MEDIUMskills/pymc/references/workflows.md45# ==========================COMMENT
MEDIUMskills/pymc/references/workflows.md55# ============COMMENT
MEDIUMskills/pymc/references/workflows.md71# ====================COMMENT
MEDIUMskills/pymc/references/workflows.md93# ==============================COMMENT
MEDIUMskills/pymc/references/workflows.md103# ==================COMMENT
MEDIUMskills/pymc/references/workflows.md115# ============================COMMENT
MEDIUMskills/pymc/references/workflows.md136# ===============COMMENT
MEDIUMskills/pymc/assets/hierarchical_model_template.py16# =============================================================================COMMENT
MEDIUMskills/pymc/assets/hierarchical_model_template.py18# =============================================================================COMMENT
MEDIUMskills/pymc/assets/hierarchical_model_template.py51# =============================================================================COMMENT
MEDIUMskills/pymc/assets/hierarchical_model_template.py53# =============================================================================COMMENT
MEDIUMskills/pymc/assets/hierarchical_model_template.py96# =============================================================================COMMENT
MEDIUMskills/pymc/assets/hierarchical_model_template.py98# =============================================================================COMMENT
MEDIUMskills/pymc/assets/hierarchical_model_template.py112# =============================================================================COMMENT
MEDIUMskills/pymc/assets/hierarchical_model_template.py114# =============================================================================COMMENT
MEDIUMskills/pymc/assets/hierarchical_model_template.py132# =============================================================================COMMENT
MEDIUMskills/pymc/assets/hierarchical_model_template.py134# =============================================================================COMMENT
MEDIUMskills/pymc/assets/hierarchical_model_template.py182# =============================================================================COMMENT
MEDIUMskills/pymc/assets/hierarchical_model_template.py184# =============================================================================COMMENT
MEDIUMskills/pymc/assets/hierarchical_model_template.py198# =============================================================================COMMENT
MEDIUMskills/pymc/assets/hierarchical_model_template.py200# =============================================================================COMMENT
MEDIUMskills/pymc/assets/hierarchical_model_template.py262# =============================================================================COMMENT
MEDIUMskills/pymc/assets/hierarchical_model_template.py264# =============================================================================COMMENT
MEDIUMskills/pymc/assets/hierarchical_model_template.py320# =============================================================================COMMENT
MEDIUMskills/pymc/assets/hierarchical_model_template.py322# =============================================================================COMMENT
MEDIUMskills/pymc/assets/linear_regression_template.py16# =============================================================================COMMENT
MEDIUMskills/pymc/assets/linear_regression_template.py18# =============================================================================COMMENT
MEDIUMskills/pymc/assets/linear_regression_template.py41# =============================================================================COMMENT
MEDIUMskills/pymc/assets/linear_regression_template.py43# =============================================================================COMMENT
MEDIUMskills/pymc/assets/linear_regression_template.py69# =============================================================================COMMENT
MEDIUMskills/pymc/assets/linear_regression_template.py71# =============================================================================COMMENT
MEDIUMskills/pymc/assets/linear_regression_template.py85# =============================================================================COMMENT
MEDIUMskills/pymc/assets/linear_regression_template.py87# =============================================================================COMMENT
MEDIUMskills/pymc/assets/linear_regression_template.py106# =============================================================================COMMENT
MEDIUMskills/pymc/assets/linear_regression_template.py108# =============================================================================COMMENT
MEDIUMskills/pymc/assets/linear_regression_template.py149# =============================================================================COMMENT
MEDIUMskills/pymc/assets/linear_regression_template.py151# =============================================================================COMMENT
MEDIUMskills/pymc/assets/linear_regression_template.py165# =============================================================================COMMENT
MEDIUMskills/pymc/assets/linear_regression_template.py167# =============================================================================COMMENT
MEDIUMskills/pymc/assets/linear_regression_template.py195# =============================================================================COMMENT
MEDIUMskills/pymc/assets/linear_regression_template.py197# =============================================================================COMMENT
MEDIUMskills/pymc/assets/linear_regression_template.py230# =============================================================================COMMENT
MEDIUMskills/pymc/assets/linear_regression_template.py232# =============================================================================COMMENT
MEDIUMskills/onekgpd/scripts/onekgpd_meta.py36# ---------------------------------------------------------------------------COMMENT
MEDIUMskills/onekgpd/scripts/onekgpd_meta.py38# ---------------------------------------------------------------------------COMMENT
MEDIUMskills/onekgpd/scripts/onekgpd_meta.py53# ---------------------------------------------------------------------------COMMENT
MEDIUMskills/onekgpd/scripts/onekgpd_meta.py55# ---------------------------------------------------------------------------COMMENT
MEDIUMskills/onekgpd/scripts/onekgpd_meta.py90# ---------------------------------------------------------------------------COMMENT
MEDIUMskills/onekgpd/scripts/onekgpd_meta.py92# ---------------------------------------------------------------------------COMMENT
MEDIUMskills/onekgpd/scripts/onekgpd_meta.py156# ---------------------------------------------------------------------------COMMENT
MEDIUMskills/onekgpd/scripts/onekgpd_meta.py158# ---------------------------------------------------------------------------COMMENT
MEDIUMskills/onekgpd/scripts/onekgpd_meta.py196# ---------------------------------------------------------------------------COMMENT
MEDIUMskills/onekgpd/scripts/onekgpd_meta.py198# ---------------------------------------------------------------------------COMMENT
MEDIUMskills/onekgpd/scripts/onekgpd_meta.py426# ---------------------------------------------------------------------------COMMENT
MEDIUMskills/onekgpd/scripts/onekgpd_meta.py428# ---------------------------------------------------------------------------COMMENT
MEDIUMskills/onekgpd/scripts/onekgpd_api.py47# ---------------------------------------------------------------------------COMMENT
MEDIUMskills/onekgpd/scripts/onekgpd_api.py49# ---------------------------------------------------------------------------COMMENT
MEDIUMskills/onekgpd/scripts/onekgpd_api.py60# ---------------------------------------------------------------------------COMMENT
118 more matches not shown…
Hyper-Verbose Identifiers362 hits · 383 pts
SeverityFileLineSnippetContext
LOWtests/test_research_lookup.py54 def test_default_backend_is_search_and_parallel_alias_is_research(self, _which):CODE
LOWtests/test_research_lookup.py63 def test_chat_is_available_but_never_selected_by_default(self, _which):CODE
LOWtests/test_research_lookup.py72 def test_explicit_chat_preserves_content_basis_and_citations(self, _which):CODE
LOWtests/test_research_lookup.py124 def test_parser_and_class_default_to_sixty_references(self, _which):CODE
LOWtests/test_research_lookup.py138 def test_nonacademic_lookup_uses_one_search_without_extract(self, _which):CODE
LOWtests/test_research_lookup.py164 def test_academic_lookup_runs_facets_and_batched_extract(self, _which):CODE
LOWtests/test_research_lookup.py234 def test_perplexity_failure_fallback_is_opt_in(self, _which):CODE
LOWtests/test_research_lookup.py258 def test_deduplication_merges_doi_url_and_title_records(self):CODE
LOWtests/test_research_lookup.py281 def test_packet_has_manuscript_artifacts_and_never_pads_shortfall(self):CODE
LOWtests/test_research_lookup.py314 def test_retracted_reference_is_marked_for_exclusion(self):CODE
LOWtests/test_research_lookup.py337 def test_save_packet_writes_all_expected_artifacts(self):CODE
LOWtests/test_research_lookup.py369 def test_existing_citation_extraction_remains_available(self):CODE
LOWskills/qiskit/references/patterns.md449def cost_function_with_tracking(params):CODE
LOWskills/pymc/scripts/model_comparison.py293def cross_validation_comparison(models_dict: Dict[str, Any],CODE
LOWskills/research-lookup/scripts/research_lookup.py370 def _rank_sources_for_extraction(CODE
LOWskills/research-lookup/scripts/research_lookup.py884 def _extract_citations_from_text(text: str) -> list[dict[str, str]]:CODE
LOWskills/geomaster/references/scientific-domains.md14def coastal_vulnerability_index(dem_path, shoreline_path, output_path):CODE
LOWskills/geomaster/references/scientific-domains.md350def estimate_biomass_from_lidar(chm_path, plot_data):CODE
LOWskills/geomaster/references/industry-applications.md221def power_line_corridor_analysis(power_lines_path, vegetation_height_path, buffer_distance=50):CODE
LOWskills/geomaster/references/advanced-gis.md176def emerging_hot_spot_analysis(cube, k=8):CODE
LOWskills/geomaster/references/machine-learning.md18def train_random_forest_classifier(raster_path, training_gdf):CODE
LOWskills/onekgpd/scripts/onekgpd_meta.py272def cmd_list_superpopulations(args) -> None:CODE
LOWskills/onekgpd/scripts/onekgpd_meta.py328def cmd_superpopulation_summary(args) -> None:CODE
LOWskills/onekgpd/scripts/onekgpd_meta.py376def cmd_select_samples_by_population(args) -> None:CODE
LOWskills/onekgpd/scripts/onekgpd_api.py442def cmd_count_variants_in_samples(args) -> None:CODE
LOWskills/onekgpd/scripts/onekgpd_api.py450def cmd_select_variants_in_samples(args) -> None:CODE
LOWskills/onekgpd/scripts/onekgpd_api.py539def cmd_count_samples_hom_ref(args) -> None:CODE
LOWskills/onekgpd/scripts/onekgpd_api.py568def cmd_select_samples_hom_ref(args) -> None:CODE
LOWskills/dask/references/dataframes.md140def custom_partition_function(partition_df):CODE
LOW…ills/exploratory-data-analysis/scripts/eda_analyzer.py251def analyze_general_scientific(filepath, extension):CODE
LOWskills/experimental-design/scripts/randomization.py89def stratified_block_randomization(strata, arms=("treatment", "control"),CODE
LOWskills/iso-13485-certification/scripts/gap_analyzer.py291 def _generate_recommendations(self, missing_procedures: List[Dict],CODE
LOWskills/esm/references/workflows.md475def predict_function_generative(sequence):CODE
LOWskills/esm/references/workflows.md491def predict_function_embedding(sequence, function_classifier):CODE
LOWskills/esm/references/esm3-api.md318def generate_with_temperature_schedule(model, protein, temperatures):CODE
LOWskills/esm/references/esm-c-api.md129def batch_encode_variable_length(model, sequences, max_batch_size=32):CODE
LOWskills/esm/references/esm-c-api.md366def get_per_residue_embeddings(model, sequence):CODE
LOWskills/esm/references/esm-c-api.md412def efficient_batch_processing(model, sequences, batch_size=32):CODE
LOW…scientific-schematics/scripts/generate_schematic_ai.py214 def _extract_image_from_response(self, response: Dict[str, Any]) -> Optional[bytes]:CODE
LOWskills/deeptools/scripts/workflow_generator.py85def generate_chipseq_qc_workflow(output_file, params):CODE
LOWskills/deeptools/scripts/workflow_generator.py162def generate_chipseq_analysis_workflow(output_file, params):STRING
LOWskills/deeptools/scripts/workflow_generator.py283def generate_rnaseq_coverage_workflow(output_file, params):STRING
LOWskills/deeptools/scripts/workflow_generator.py334def generate_atacseq_workflow(output_file, params):STRING
LOWskills/fluidsim/references/advanced_features.md291 def _complete_params_with_default(params):CODE
LOW…s/citation-management/scripts/generate_schematic_ai.py214 def _extract_image_from_response(self, response: Dict[str, Any]) -> Optional[bytes]:CODE
LOW…ills/citation-management/scripts/validate_citations.py303 def parse_manuscript_citations(self, filepath: str) -> List[str]:CODE
LOWskills/citation-management/scripts/search_pubmed.py154 def _extract_metadata_from_xml(self, article: ET.Element) -> Optional[Dict]:CODE
LOWskills/markitdown/scripts/generate_schematic_ai.py214 def _extract_image_from_response(self, response: Dict[str, Any]) -> Optional[bytes]:CODE
LOWskills/markitdown/scripts/convert_literature.py19def extract_metadata_from_filename(filename: str) -> Dict[str, str]:CODE
LOWskills/pytdc/scripts/benchmark_evaluation.py43def single_dataset_evaluation(group, dataset_name='Caco2_Wang'):CODE
LOWskills/pytdc/scripts/benchmark_evaluation.py102def multiple_datasets_evaluation(group):CODE
LOWskills/pytdc/scripts/benchmark_evaluation.py247def leaderboard_submission_guide():STRING
LOWskills/pytdc/scripts/molecular_generation.py156def goal_directed_generation_template():CODE
LOWskills/pytdc/scripts/molecular_generation.py220def distribution_learning_example(train_smiles):STRING
LOWskills/pytdc/scripts/molecular_generation.py309def constraint_satisfaction_example():STRING
LOWskills/xlsx/scripts/office/validators/docx.py66 def validate_whitespace_preservation(self):CODE
LOWskills/xlsx/scripts/office/validators/docx.py163 def count_paragraphs_in_unpacked(self):CODE
LOWskills/xlsx/scripts/office/validators/docx.py179 def count_paragraphs_in_original(self):CODE
LOWskills/xlsx/scripts/office/validators/redlining.py198 def _remove_author_tracked_changes(self, root):CODE
LOWskills/xlsx/scripts/office/validators/pptx.py104 def validate_slide_layout_ids(self):CODE
302 more matches not shown…
Magic Placeholder Names69 hits · 319 pts
SeverityFileLineSnippetContext
HIGHSECURITY.md1474 > The references/data-sources.md file contains multiple code examples using placeholder API key variables (YOUR_API_KECODE
HIGH…lls/benchling-integration/references/authentication.md301 -u "your_api_key:" \CODE
HIGH…lls/benchling-integration/references/authentication.md321 auth_method=ApiKeyAuth("your_api_key")CODE
HIGH…lls/benchling-integration/references/authentication.md381 auth_method=ApiKeyAuth("your_api_key"),CODE
HIGH…ills/benchling-integration/references/api_endpoints.md26 -u "your_api_key:"CODE
HIGH…ills/benchling-integration/references/sdk_reference.md571 auth_method=ApiKeyAuth("your_api_key"),CODE
HIGH…ills/benchling-integration/references/sdk_reference.md578 auth_method=ApiKeyAuth("your_api_key"),CODE
HIGHskills/geomaster/references/data-sources.md179 'key': YOUR_API_KEYSTRING
HIGHskills/geomaster/references/data-sources.md208 'appid': YOUR_API_KEYSTRING
HIGH…scientific-schematics/scripts/generate_schematic_ai.py784 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGH…ls/scientific-schematics/scripts/generate_schematic.py99 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGHskills/pyzotero/SKILL.md27ZOTERO_API_KEY=your_api_keyCODE
HIGHskills/database-lookup/references/bea.md13- Pass as query parameter: `&UserID=YOUR_API_KEY`CODE
HIGHskills/database-lookup/references/lincs-l1000.md13- Pass via header: `user_key: YOUR_API_KEY`CODE
HIGHskills/database-lookup/references/lincs-l1000.md36curl -H "user_key: YOUR_API_KEY" \CODE
HIGHskills/database-lookup/references/lincs-l1000.md40curl -H "user_key: YOUR_API_KEY" \CODE
HIGHskills/database-lookup/references/lincs-l1000.md44curl -H "user_key: YOUR_API_KEY" \CODE
HIGHskills/database-lookup/references/lincs-l1000.md48curl -H "user_key: YOUR_API_KEY" \CODE
HIGHskills/database-lookup/references/omim.md10- Pass as query parameter: `?apiKey=YOUR_API_KEY`CODE
HIGHskills/database-lookup/references/addgene.md10Pass as: `Authorization: Token <your_api_key>`CODE
HIGHskills/citation-management/references/pubmed_search.md385 api_key=YOUR_API_KEYCODE
HIGHskills/citation-management/references/pubmed_search.md418 api_key=YOUR_API_KEYCODE
HIGHskills/citation-management/references/pubmed_search.md442 api_key=YOUR_API_KEYCODE
HIGH…s/citation-management/scripts/generate_schematic_ai.py784 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGH…ills/citation-management/scripts/generate_schematic.py99 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGHskills/markitdown/scripts/generate_schematic_ai.py784 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGHskills/markitdown/scripts/generate_schematic.py99 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGHskills/infographics/scripts/generate_infographic_ai.py1286 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGHskills/infographics/scripts/generate_infographic.py182 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGHskills/pptx-posters/scripts/generate_schematic_ai.py784 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGHskills/pptx-posters/scripts/generate_schematic.py99 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGHskills/treatment-plans/scripts/generate_schematic_ai.py784 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGHskills/treatment-plans/scripts/generate_schematic.py99 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGH…ls/scientific-writing/scripts/generate_schematic_ai.py784 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGHskills/scientific-writing/scripts/generate_schematic.py99 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGHskills/scientific-writing/scripts/generate_image.py108 print("OPENROUTER_API_KEY=your-api-key-here")CODE
HIGHskills/scientific-writing/scripts/generate_image.py110 print("export OPENROUTER_API_KEY=your-api-key-here")CODE
HIGH…ical-decision-support/scripts/generate_schematic_ai.py784 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGH…linical-decision-support/scripts/generate_schematic.py99 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGHskills/paper-lookup/references/core.md15- **Header:** `Authorization: Bearer YOUR_API_KEY`CODE
HIGHskills/paper-lookup/references/core.md16- **Query param:** `?api_key=YOUR_API_KEY`CODE
HIGH…lls/literature-review/scripts/generate_schematic_ai.py784 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGHskills/literature-review/scripts/generate_schematic.py99 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGH…ls/scholar-evaluation/scripts/generate_schematic_ai.py784 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGHskills/scholar-evaluation/scripts/generate_schematic.py99 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGHskills/cirq/references/hardware.md173# export IONQ_API_KEY=your_api_keyCOMMENT
HIGHskills/cirq/references/hardware.md493export IONQ_API_KEY=your_api_keyCODE
HIGHskills/latex-posters/scripts/generate_schematic_ai.py784 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGHskills/latex-posters/scripts/generate_schematic.py99 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGHskills/adaptyv/SKILL.md51ADAPTYV_API_KEY=your_api_keyCODE
HIGHskills/venue-templates/scripts/generate_schematic_ai.py784 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGHskills/venue-templates/scripts/generate_schematic.py99 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGHskills/pytorch-lightning/references/logging.md103 api_key="YOUR_API_KEY",CODE
HIGH…ills/clinical-reports/scripts/generate_schematic_ai.py784 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGHskills/clinical-reports/scripts/generate_schematic.py99 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGH…lls/scientific-slides/scripts/generate_schematic_ai.py784 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGH…s/scientific-slides/scripts/generate_slide_image_ai.py704 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGHskills/scientific-slides/scripts/generate_schematic.py99 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGH…ills/scientific-slides/scripts/generate_slide_image.py96 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGHskills/tamarind/SKILL.md51export TAMARIND_API_KEY="your_api_key"CODE
9 more matches not shown…
Cross-Language Confusion44 hits · 261 pts
SeverityFileLineSnippetContext
HIGHskills/research-lookup/scripts/research_lookup.py126 "Find conflicting, contradictory, null, negative, replication, and limitation "CODE
HIGHskills/xlsx/scripts/office/soffice.py150 if (sv[0] >= 0 && sv[0] < 1024) {CODE
HIGHskills/xlsx/scripts/office/soffice.py169 if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) {CODE
HIGHskills/xlsx/scripts/office/soffice.py178 if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) {CODE
HIGHskills/xlsx/scripts/office/soffice.py192 if (fd >= 0 && fd < 1024 && is_shimmed[fd]) {CODE
HIGH…recasting/examples/global-temperature/generate_html.py403 ...Array(nActual).fill(null),CODE
HIGH…recasting/examples/global-temperature/generate_html.py411 dataUsed.push(step.historical_values[i]);CODE
HIGH…recasting/examples/global-temperature/generate_html.py413 dataUsed.push(null);CODE
HIGH…recasting/examples/global-temperature/generate_html.py413 dataUsed.push(null);CODE
HIGH…recasting/examples/global-temperature/generate_html.py427 if (forecastIdx >= 0 && forecastIdx < nForecast) {{CODE
HIGH…recasting/examples/global-temperature/generate_html.py428 q90Lower.push(step.q10[forecastIdx]);CODE
HIGH…recasting/examples/global-temperature/generate_html.py429 q90Upper.push(step.q90[forecastIdx]);CODE
HIGH…recasting/examples/global-temperature/generate_html.py430 q80Lower.push(step.q20[forecastIdx]);CODE
HIGH…recasting/examples/global-temperature/generate_html.py431 q80Upper.push(step.q80[forecastIdx]);CODE
HIGH…recasting/examples/global-temperature/generate_html.py433 q90Lower.push(null);CODE
HIGH…recasting/examples/global-temperature/generate_html.py433 q90Lower.push(null);CODE
HIGH…recasting/examples/global-temperature/generate_html.py434 q90Upper.push(null);CODE
HIGH…recasting/examples/global-temperature/generate_html.py434 q90Upper.push(null);CODE
HIGH…recasting/examples/global-temperature/generate_html.py435 q80Lower.push(null);CODE
HIGH…recasting/examples/global-temperature/generate_html.py435 q80Lower.push(null);CODE
HIGH…recasting/examples/global-temperature/generate_html.py436 q80Upper.push(null);CODE
HIGH…recasting/examples/global-temperature/generate_html.py436 q80Upper.push(null);CODE
HIGH…recasting/examples/global-temperature/generate_html.py448 if (forecastIdx >= 0 && forecastIdx < nForecast) {{CODE
HIGH…recasting/examples/global-temperature/generate_html.py449 forecastData.push(step.point_forecast[forecastIdx]);CODE
HIGH…recasting/examples/global-temperature/generate_html.py451 forecastData.push(null);CODE
HIGH…recasting/examples/global-temperature/generate_html.py451 forecastData.push(null);CODE
HIGH…recasting/examples/global-temperature/generate_html.py227 let chart = null;CODE
HIGH…recasting/examples/global-temperature/generate_html.py229 let playInterval = null;CODE
HIGH…recasting/examples/global-temperature/generate_html.py275 data: [...Array(animationData.actual_data.dates.length).fill(null), ...finalStep.point_forecCODE
HIGHskills/treatment-plans/scripts/check_completeness.py257 python check_completeness.py plan.tex && echo "Complete"CODE
HIGH…lls/treatment-plans/scripts/validate_treatment_plan.py313 python validate_treatment_plan.py plan.tex && echo "Quality check passed"CODE
HIGHskills/pptx/scripts/office/soffice.py116 if (sv[0] >= 0 && sv[0] < 1024) {CODE
HIGHskills/pptx/scripts/office/soffice.py135 if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) {CODE
HIGHskills/pptx/scripts/office/soffice.py144 if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) {CODE
HIGHskills/pptx/scripts/office/soffice.py158 if (fd >= 0 && fd < 1024 && is_shimmed[fd]) {CODE
HIGHskills/pyopenms/scripts/theoretical_spectrum.py49 print(f"Peptide: {seq.toString()} ({len(spec)} fragment peaks)")CODE
HIGHskills/pyopenms/scripts/mass_calculator.py69 print(f"Peptide: {seq.toString()}")CODE
HIGHskills/pyopenms/scripts/mass_calculator.py70 print(f"Formula: {formula.toString()}")CODE
HIGHskills/pyopenms/scripts/mass_calculator.py81 print(f"\nFormula: {formula.toString()}")CODE
HIGHskills/pyopenms/scripts/digest_protein.py74 pep_str = pep.toString()CODE
HIGHskills/docx/scripts/office/soffice.py116 if (sv[0] >= 0 && sv[0] < 1024) {CODE
HIGHskills/docx/scripts/office/soffice.py135 if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) {CODE
HIGHskills/docx/scripts/office/soffice.py144 if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) {CODE
HIGHskills/docx/scripts/office/soffice.py158 if (fd >= 0 && fd < 1024 && is_shimmed[fd]) {CODE
Deep Nesting229 hits · 221 pts
SeverityFileLineSnippetContext
LOWscan_pr_skills.py99CODE
LOWscan_skills.py58CODE
LOWskills/pymc/scripts/model_comparison.py27CODE
LOWskills/pymc/scripts/model_comparison.py120CODE
LOWskills/research-lookup/scripts/manuscript_packet.py433CODE
LOWskills/research-lookup/scripts/research_lookup.py603CODE
LOW…ls/get-available-resources/scripts/detect_resources.py82CODE
LOW…ls/get-available-resources/scripts/detect_resources.py117CODE
LOW…ls/get-available-resources/scripts/detect_resources.py150CODE
LOW…ls/get-available-resources/scripts/detect_resources.py274CODE
LOW…ills/exploratory-data-analysis/scripts/eda_analyzer.py215CODE
LOW…ills/exploratory-data-analysis/scripts/eda_analyzer.py251CODE
LOW…ills/exploratory-data-analysis/scripts/eda_analyzer.py335CODE
LOW…ills/exploratory-data-analysis/scripts/eda_analyzer.py381CODE
LOWskills/iso-13485-certification/scripts/gap_analyzer.py197CODE
LOW…scientific-schematics/scripts/generate_schematic_ai.py214CODE
LOW…scientific-schematics/scripts/generate_schematic_ai.py321CODE
LOW…scientific-schematics/scripts/generate_schematic_ai.py399CODE
LOWskills/deeptools/scripts/validate_files.py46CODE
LOWskills/deeptools/scripts/workflow_generator.py422CODE
LOWskills/medchem/scripts/filter_molecules.py28CODE
LOWskills/pymatgen/scripts/structure_analyzer.py36CODE
LOWskills/pymatgen/scripts/structure_analyzer.py194CODE
LOWskills/pymatgen/scripts/structure_converter.py87CODE
LOWskills/pymatgen/scripts/phase_diagram_generator.py48CODE
LOWskills/citation-management/scripts/extract_metadata.py141CODE
LOWskills/citation-management/scripts/extract_metadata.py213CODE
LOW…s/citation-management/scripts/generate_schematic_ai.py214CODE
LOW…s/citation-management/scripts/generate_schematic_ai.py321CODE
LOW…s/citation-management/scripts/generate_schematic_ai.py399CODE
LOWskills/citation-management/scripts/format_bibtex.py201CODE
LOWskills/citation-management/scripts/format_bibtex.py213CODE
LOW…s/citation-management/scripts/search_google_scholar.py47CODE
LOW…ills/citation-management/scripts/validate_citations.py95CODE
LOW…ills/citation-management/scripts/validate_citations.py341CODE
LOWskills/citation-management/scripts/search_pubmed.py98CODE
LOWskills/citation-management/scripts/search_pubmed.py154CODE
LOWskills/pydicom/scripts/anonymize_dicom.py40CODE
LOWskills/pydicom/scripts/dicom_to_image.py52CODE
LOWskills/markitdown/scripts/generate_schematic_ai.py214CODE
LOWskills/markitdown/scripts/generate_schematic_ai.py321CODE
LOWskills/markitdown/scripts/generate_schematic_ai.py399CODE
LOWskills/xlsx/scripts/recalc.py73CODE
LOWskills/xlsx/scripts/office/pack.py24CODE
LOWskills/xlsx/scripts/office/pack.py108CODE
LOWskills/xlsx/scripts/office/validators/docx.py66CODE
LOWskills/xlsx/scripts/office/validators/docx.py112CODE
LOWskills/xlsx/scripts/office/validators/docx.py254CODE
LOWskills/xlsx/scripts/office/validators/docx.py298CODE
LOWskills/xlsx/scripts/office/validators/docx.py391CODE
LOWskills/xlsx/scripts/office/validators/redlining.py127CODE
LOWskills/xlsx/scripts/office/validators/redlining.py198CODE
LOWskills/xlsx/scripts/office/validators/pptx.py62CODE
LOWskills/xlsx/scripts/office/validators/pptx.py104CODE
LOWskills/xlsx/scripts/office/validators/pptx.py210CODE
LOWskills/xlsx/scripts/office/validators/base.py115CODE
LOWskills/xlsx/scripts/office/validators/base.py199CODE
LOWskills/xlsx/scripts/office/validators/base.py289CODE
LOWskills/xlsx/scripts/office/validators/base.py385CODE
LOWskills/xlsx/scripts/office/validators/base.py469CODE
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Unused Imports102 hits · 98 pts
SeverityFileLineSnippetContext
LOWscan_pr_skills.py15CODE
LOWtests/test_research_lookup.py3CODE
LOWskills/pymc/scripts/model_comparison.py22CODE
LOWskills/pymc/assets/hierarchical_model_template.py13CODE
LOWskills/pymc/assets/linear_regression_template.py13CODE
LOWskills/research-lookup/scripts/manuscript_packet.py3CODE
LOWskills/research-lookup/scripts/research_lookup.py9CODE
LOWskills/onekgpd/scripts/onekgpd_meta.py25CODE
LOWskills/onekgpd/scripts/onekgpd_api.py28CODE
LOW…ls/get-available-resources/scripts/detect_resources.py19CODE
LOW…ls/get-available-resources/scripts/detect_resources.py20CODE
LOWskills/experimental-design/scripts/doe_designs.py25CODE
LOWskills/experimental-design/scripts/randomization.py20CODE
LOWskills/iso-13485-certification/scripts/gap_analyzer.py16CODE
LOWskills/deeptools/scripts/validate_files.py12CODE
LOWskills/medchem/scripts/filter_molecules.py14CODE
LOWskills/pymatgen/scripts/structure_analyzer.py25CODE
LOWskills/pathway-enrichment/scripts/run_enrichment.py29CODE
LOWskills/citation-management/scripts/format_bibtex.py10CODE
LOWskills/markitdown/scripts/convert_literature.py14CODE
LOWskills/pytdc/scripts/load_and_split_data.py15CODE
LOWskills/xlsx/scripts/office/validators/__init__.py5CODE
LOWskills/xlsx/scripts/office/validators/__init__.py6CODE
LOWskills/xlsx/scripts/office/validators/__init__.py7CODE
LOWskills/xlsx/scripts/office/validators/__init__.py8CODE
LOWskills/exa-search/tests/test_exa_search.py12CODE
LOWskills/exa-search/scripts/exa_search.py16CODE
LOWskills/exa-search/scripts/exa_extract.py15CODE
LOWskills/autoskill/tests/test_e2e.py9CODE
LOW…ing/examples/covariates-forecasting/demo_covariates.py28CODE
LOW…casting/examples/anomaly-detection/detect_anomalies.py17CODE
LOW…orecasting/examples/global-temperature/run_forecast.py7CODE
LOW…recasting/examples/global-temperature/generate_html.py9CODE
LOW…ting/examples/global-temperature/visualize_forecast.py14CODE
LOW…examples/global-temperature/generate_animation_data.py11CODE
LOW…orecasting/examples/global-temperature/generate_gif.py8CODE
LOWskills/timesfm-forecasting/scripts/forecast_csv.py21CODE
LOWskills/timesfm-forecasting/scripts/check_system.py16CODE
LOWskills/arbor/scripts/tree.py34CODE
LOW…ills/statistical-analysis/scripts/assumption_checks.py16CODE
LOW…ills/statistical-analysis/scripts/assumption_checks.py17CODE
LOW…ical-decision-support/scripts/validate_cds_document.py19CODE
LOW…inical-decision-support/scripts/build_decision_tree.py12CODE
LOWskills/diffdock/scripts/analyze_results.py17CODE
LOWskills/diffdock/scripts/analyze_results.py19CODE
LOWskills/literature-review/scripts/verify_citations.py11CODE
LOWskills/scholar-evaluation/scripts/calculate_scores.py20CODE
LOWskills/pptx/scripts/office/validators/__init__.py5CODE
LOWskills/pptx/scripts/office/validators/__init__.py6CODE
LOWskills/pptx/scripts/office/validators/__init__.py7CODE
LOWskills/pptx/scripts/office/validators/__init__.py8CODE
LOWskills/primekg/scripts/query_primekg.py3CODE
LOW…ills/open-notebook/scripts/test_open_notebook_skill.py11CODE
LOW…et-research-reports/scripts/generate_market_visuals.py23CODE
LOWskills/deepchem/scripts/predict_solubility.py15CODE
LOWskills/scvelo/scripts/rna_velocity_workflow.py14CODE
LOWskills/scvelo/scripts/rna_velocity_workflow.py17CODE
LOWskills/simpy/scripts/resource_monitor.py11CODE
LOWskills/venue-templates/scripts/validate_format.py15CODE
LOWskills/venue-templates/scripts/query_template.py14CODE
42 more matches not shown…
Verbosity Indicators54 hits · 93 pts
SeverityFileLineSnippetContext
LOWskills/deeptools/scripts/workflow_generator.py127# Step 2: Coverage assessmentCOMMENT
LOWskills/deeptools/scripts/workflow_generator.py135# Step 3: Fragment size (for paired-end data)COMMENT
LOWskills/deeptools/scripts/workflow_generator.py142# Step 4: ChIP signal strengthCOMMENT
LOWskills/deeptools/scripts/workflow_generator.py368# Step 2: Generate coverage trackCOMMENT
LOWskills/deeptools/scripts/workflow_generator.py378# Step 3: Fragment size analysisCOMMENT
LOWskills/deeptools/scripts/workflow_generator.py385# Step 4: Compute matrix at peaks (if peaks provided)COMMENT
LOWskills/deeptools/scripts/workflow_generator.py106# Step 1: Correlation analysisCOMMENT
LOWskills/deeptools/scripts/workflow_generator.py185# Step 1: Generate normalized coverage tracksCOMMENT
LOWskills/deeptools/scripts/workflow_generator.py208# Step 2: Create log2 ratio trackCOMMENT
LOWskills/deeptools/scripts/workflow_generator.py221# Step 3: Compute matrix around TSSCOMMENT
LOWskills/deeptools/scripts/workflow_generator.py235# Step 4: Generate heatmapCOMMENT
LOWskills/deeptools/scripts/workflow_generator.py248# Step 5: Generate profile plotCOMMENT
LOWskills/deeptools/scripts/workflow_generator.py260# Step 6: Enrichment at peaks (if peaks provided)COMMENT
LOWskills/deeptools/scripts/workflow_generator.py355# Step 1: Shift reads for Tn5 correctionCOMMENT
LOW…forecasting/examples/global-temperature/run_example.sh26# Step 1: Preflight checkCOMMENT
LOW…forecasting/examples/global-temperature/run_example.sh34# Step 2: Run forecastCOMMENT
LOW…forecasting/examples/global-temperature/run_example.sh40# Step 3: Generate visualizationCOMMENT
LOW…ls/opentrons-integration/scripts/pcr_setup_template.py80 # Step 1: Distribute master mixCOMMENT
LOW…ls/opentrons-integration/scripts/pcr_setup_template.py90 # Step 2: Add template DNACOMMENT
LOW…ntrons-integration/scripts/serial_dilution_template.py65 # Step 1: Add diluent to all wells except first columnCOMMENT
LOW…ntrons-integration/scripts/serial_dilution_template.py75 # Step 2: Add stock solution to first columnCOMMENT
LOW…ntrons-integration/scripts/serial_dilution_template.py84 # Step 3: Perform serial dilutionCOMMENT
LOWskills/bioservices/scripts/compound_cross_reference.py337 # Step 1: Search KEGGSTRING
LOWskills/bioservices/scripts/compound_cross_reference.py343 # Step 2: Get KEGG detailsSTRING
LOWskills/bioservices/scripts/compound_cross_reference.py346 # Step 3: Map to ChEMBLSTRING
LOWskills/bioservices/scripts/compound_cross_reference.py349 # Step 4: Get ChEBI detailsSTRING
LOWskills/bioservices/scripts/compound_cross_reference.py354 # Step 5: Get ChEMBL detailsSTRING
LOWskills/bioservices/scripts/protein_analysis_workflow.py388 # Step 1: Search proteinSTRING
LOWskills/bioservices/scripts/protein_analysis_workflow.py394 # Step 2: Retrieve sequenceSTRING
LOWskills/bioservices/scripts/protein_analysis_workflow.py399 # Step 3: BLAST searchSTRING
LOWskills/bioservices/scripts/protein_analysis_workflow.py404 # Step 4: Pathway discoverySTRING
LOWskills/bioservices/scripts/protein_analysis_workflow.py408 # Step 5: Interaction mappingSTRING
LOWskills/bioservices/scripts/protein_analysis_workflow.py411 # Step 6: GO annotationsSTRING
LOWskills/gget/scripts/batch_sequence_analysis.py67 # Step 1: BLAST each sequenceCOMMENT
LOWskills/gget/scripts/batch_sequence_analysis.py90 # Step 2: Multiple sequence alignmentCOMMENT
LOWskills/gget/scripts/batch_sequence_analysis.py105 # Step 3: Structure prediction (optional)COMMENT
LOWskills/gget/scripts/gene_analysis.py27 # Step 1: Search for the geneCOMMENT
LOWskills/gget/scripts/gene_analysis.py39 # Step 2: Get detailed informationCOMMENT
LOWskills/gget/scripts/gene_analysis.py50 # Step 3: Get sequencesCOMMENT
LOWskills/gget/scripts/gene_analysis.py63 # Step 4: Get tissue expressionCOMMENT
LOWskills/gget/scripts/gene_analysis.py78 # Step 5: Find correlated genesCOMMENT
LOWskills/gget/scripts/gene_analysis.py92 # Step 6: Get disease associationsCOMMENT
LOWskills/gget/scripts/gene_analysis.py105 # Step 7: Get drug associationsCOMMENT
LOW…s/neuropixels-analysis/scripts/neuropixels_pipeline.py63 # Step 1: High-pass filterCOMMENT
LOW…s/neuropixels-analysis/scripts/neuropixels_pipeline.py67 # Step 2: Detect bad channelsCOMMENT
LOW…s/neuropixels-analysis/scripts/neuropixels_pipeline.py75 # Step 3: Phase shift (for Neuropixels 1.0)COMMENT
LOW…s/neuropixels-analysis/scripts/neuropixels_pipeline.py80 # Step 4: Common median referenceCOMMENT
LOWskills/pymoo/scripts/decision_making_example.py138 # Step 1: Run optimizationCOMMENT
LOWskills/pymoo/scripts/decision_making_example.py141 # Step 2: Find extreme solutionsCOMMENT
LOWskills/pymoo/scripts/decision_making_example.py144 # Step 3: Compare different preference weightsCOMMENT
LOWskills/pymoo/scripts/decision_making_example.py147 # Step 4: Visualize selections with petal diagramCOMMENT
LOWskills/phylogenetics/scripts/phylogenetic_analysis.py234 # Step 1: Multiple Sequence AlignmentCOMMENT
LOWskills/phylogenetics/scripts/phylogenetic_analysis.py243 # Step 2: Tree InferenceCOMMENT
LOWskills/phylogenetics/scripts/phylogenetic_analysis.py256 # Step 3: VisualizationCOMMENT
Modern AI Meta-Vocabulary30 hits · 90 pts
SeverityFileLineSnippetContext
MEDIUMskills/molfeat/SKILL.md161# MACCS - Fast, good for scaffold hoppingCOMMENT
MEDIUMskills/molfeat/SKILL.md216# MACCS - Fast, scaffold-based similarityCOMMENT
MEDIUMskills/pytdc/scripts/load_and_split_data.py196 # Example 1: Single prediction with scaffold splitCOMMENT
MEDIUMskills/nextflow/references/developing.md27│ └── mypipeline.nf # the primary workflow (orchestrates subworkflows)CODE
MEDIUMskills/nextflow/references/testing.md23nf-test init # creates nf-test.config + tests/ scaffolding in a projectCODE
MEDIUMskills/nextflow/references/nf-core-tools.md120nf-core pipelines create # scaffoldCODE
MEDIUMskills/timesfm-forecasting/SKILL.md337 max_context=1024, # Max context window (truncates longer series)CODE
MEDIUMskills/datamol/SKILL.md278# Get Bemis-Murcko scaffold (core structure)COMMENT
MEDIUMskills/datamol/SKILL.md285# Group compounds by scaffoldCOMMENT
MEDIUMskills/datamol/SKILL.md291# Count scaffold frequencyCOMMENT
MEDIUMskills/datamol/SKILL.md295# Create scaffold-to-molecules mappingCOMMENT
MEDIUMskills/datamol/SKILL.md560# Group by scaffoldCOMMENT
MEDIUMskills/datamol/SKILL.md571# Analyze each scaffold seriesCOMMENT
MEDIUMskills/datamol/references/fragments_scaffolds.md3## Scaffolds Module (`datamol.scaffold`)COMMENT
MEDIUMskills/datamol/references/fragments_scaffolds.md28# Count scaffold frequencyCOMMENT
MEDIUMskills/datamol/references/fragments_scaffolds.md36#### `dm.scaffold.fuzzy_scaffolding(mol, ...)`COMMENT
MEDIUMskills/datamol/references/fragments_scaffolds.md45# Group compounds by scaffoldCOMMENT
MEDIUMskills/datamol/references/fragments_scaffolds.md58# Group by scaffold and analyze activityCOMMENT
MEDIUMskills/markdown-mermaid-writing/templates/kanban.md127| [Work item] | [Person] | [Person] | [#NNN](../../docs/project/pr/pr-00000001-agentic-docs-and-monorepo-modernization.mCODE
MEDIUMskills/markdown-mermaid-writing/templates/kanban.md138| [Work item] | [Person] | [Date] | [N days] | [#NNN](../../docs/project/pr/pr-00000001-agentic-docs-and-monorepo-mCODE
MEDIUMskills/markdown-mermaid-writing/templates/issue.md60| **Resolved in** | [PR-#NUMBER](../../docs/project/pr/pr-00000001-agentic-docs-and-monorepo-modernization.md) orCODE
MEDIUMskills/markdown-mermaid-writing/templates/issue.md163**Fixed in:** [PR-#NUMBER](../../docs/project/pr/pr-00000001-agentic-docs-and-monorepo-modernization.md)CODE
MEDIUMskills/markdown-mermaid-writing/templates/issue.md208| **Shipped in** | [PR-#NUMBER](../../docs/project/pr/pr-00000001-agentic-docs-and-monorepo-modernization.md) or N/ACODE
MEDIUM…lls/markdown-mermaid-writing/templates/pull_request.md49| **Related issues** | [#ISSUE](../../docs/project/issues/issue-00000001-agentic-documentation-system.md), [#ISSUE2](..CODE
MEDIUMskills/rdkit/SKILL.md597# Generate Murcko scaffold hashCOMMENT
MEDIUMskills/pufferlib/references/integration.md137# Create multi-agent environmentCOMMENT
MEDIUMskills/pufferlib/references/integration.md150 # Train on multi-agent dataCOMMENT
MEDIUMskills/pufferlib/references/integration.md204# Large-scale multi-agent environmentCOMMENT
MEDIUMskills/optimize-for-gpu/references/cuvs.md422### End-to-End RAG Pipeline ExampleCOMMENT
MEDIUMskills/liteparse/references/output_formats.md141## Layout-aware RAG patternsCOMMENT
Redundant / Tautological Comments51 hits · 68 pts
SeverityFileLineSnippetContext
LOWskills/pymc/scripts/model_comparison.py104 # Check if difference is significant relative to SECOMMENT
LOW…ls/get-available-resources/scripts/detect_resources.py156 # Check if running on Apple SiliconCOMMENT
LOWskills/iso-13485-certification/scripts/gap_analyzer.py207 # Read file content (simple text reading)COMMENT
LOWskills/iso-13485-certification/scripts/gap_analyzer.py230 # Check if any keyword appears in the documentCOMMENT
LOW…scientific-schematics/scripts/generate_schematic_ai.py678 # Check if quality is acceptable - STOP EARLY if soCOMMENT
LOWskills/deeptools/scripts/validate_files.py61 # Check if start and end are integersCOMMENT
LOWskills/deeptools/scripts/validate_files.py168 # Check if any files were providedSTRING
LOWskills/deeptools/scripts/validate_files.py180 # Print resultsSTRING
LOWskills/deeptools/scripts/workflow_generator.py478 # Check if workflow was specifiedSTRING
LOWskills/citation-management/scripts/extract_metadata.py46 # Check if URLCOMMENT
LOW…s/citation-management/scripts/generate_schematic_ai.py678 # Check if quality is acceptable - STOP EARLY if soCOMMENT
LOWskills/markitdown/scripts/generate_schematic_ai.py678 # Check if quality is acceptable - STOP EARLY if soCOMMENT
LOWskills/timesfm-forecasting/scripts/check_system.py388 # Check if GPU is availableCOMMENT
LOWskills/infographics/scripts/generate_infographic_ai.py1142 # Check if quality is acceptableSTRING
LOWskills/pptx-posters/scripts/generate_schematic_ai.py678 # Check if quality is acceptable - STOP EARLY if soCOMMENT
LOWskills/treatment-plans/scripts/generate_schematic_ai.py678 # Check if quality is acceptable - STOP EARLY if soCOMMENT
LOWskills/treatment-plans/scripts/check_completeness.py295 # Read fileSTRING
LOWskills/treatment-plans/scripts/check_completeness.py305 # Display resultsSTRING
LOW…lls/treatment-plans/scripts/validate_treatment_plan.py353 # Display resultsSTRING
LOWskills/treatment-plans/scripts/timeline_generator.py334 # Check if any timeline info foundSTRING
LOW…ills/statistical-analysis/scripts/assumption_checks.py566 # Check if grouped dataCOMMENT
LOW…ls/scientific-writing/scripts/generate_schematic_ai.py678 # Check if quality is acceptable - STOP EARLY if soCOMMENT
LOW…ical-decision-support/scripts/generate_schematic_ai.py678 # Check if quality is acceptable - STOP EARLY if soCOMMENT
LOW…ical-decision-support/scripts/validate_cds_document.py215 # Check if gene appears but not in italics (\textit{} or \emph{})COMMENT
LOW…nical-decision-support/scripts/create_cohort_tables.py47 # Check if Fisher's exact is needed (expected count < 5)COMMENT
LOWskills/diffdock/scripts/analyze_results.py36 # Check if this is a single complex or batch resultsCOMMENT
LOWskills/diffdock/scripts/prepare_batch_csv.py130 # Check if it's a file path or SMILESCOMMENT
LOWskills/bioservices/scripts/protein_analysis_workflow.py76 # Display resultsCOMMENT
LOW…lls/literature-review/scripts/generate_schematic_ai.py678 # Check if quality is acceptable - STOP EARLY if soCOMMENT
LOWskills/literature-review/scripts/generate_pdf.py44 # Check if pandoc is installedCOMMENT
LOW…ls/scholar-evaluation/scripts/generate_schematic_ai.py678 # Check if quality is acceptable - STOP EARLY if soCOMMENT
LOWskills/deepchem/scripts/predict_solubility.py150 # Display resultsCOMMENT
LOWskills/latex-posters/scripts/generate_schematic_ai.py678 # Check if quality is acceptable - STOP EARLY if soCOMMENT
LOWskills/latex-posters/scripts/review_poster.sh13# Check if file argument providedCOMMENT
LOWskills/latex-posters/scripts/review_poster.sh22# Check if file existsCOMMENT
LOWskills/latex-posters/scripts/review_poster.sh93 # Check if file is too large for emailCOMMENT
LOWskills/venue-templates/scripts/generate_schematic_ai.py678 # Check if quality is acceptable - STOP EARLY if soCOMMENT
LOWskills/venue-templates/scripts/validate_format.py175 # Print resultsCOMMENT
LOW…ills/clinical-reports/scripts/generate_schematic_ai.py678 # Check if quality is acceptable - STOP EARLY if soCOMMENT
LOW…lls/scientific-slides/scripts/validate_presentation.py387 # Print resultsSTRING
LOW…lls/scientific-slides/scripts/generate_schematic_ai.py678 # Check if quality is acceptable - STOP EARLY if soCOMMENT
LOW…hypothesis-generation/scripts/generate_schematic_ai.py678 # Check if quality is acceptable - STOP EARLY if soCOMMENT
LOWskills/rdkit/scripts/similarity_search.py288 # Output resultsSTRING
LOWskills/rdkit/scripts/molecular_properties.py131 # Output resultsCOMMENT
LOWskills/stable-baselines3/scripts/custom_env_template.py135 # Check if goal is reachedCOMMENT
LOWskills/pufferlib/scripts/env_template.py102 # Check if episode is doneCOMMENT
LOWskills/pymoo/scripts/many_objective_example.py44 # Print results summaryCOMMENT
LOWskills/pymoo/scripts/single_objective_example.py45 # Print resultsCOMMENT
LOWskills/pymoo/scripts/multi_objective_example.py36 # Print results summaryCOMMENT
LOWskills/labarchive-integration/scripts/setup_config.py167 # Check if config already existsCOMMENT
LOWskills/peer-review/scripts/generate_schematic_ai.py678 # Check if quality is acceptable - STOP EARLY if soCOMMENT
AI Slop Vocabulary25 hits · 61 pts
SeverityFileLineSnippetContext
MEDIUMskills/iso-13485-certification/scripts/gap_analyzer.py249 """Generate comprehensive gap analysis report."""STRING
MEDIUM…scientific-schematics/scripts/generate_schematic_ai.py74 # Scientific diagram best practices prompt templateCOMMENT
MEDIUM…s/citation-management/scripts/generate_schematic_ai.py74 # Scientific diagram best practices prompt templateCOMMENT
MEDIUMskills/markitdown/scripts/generate_schematic_ai.py74 # Scientific diagram best practices prompt templateCOMMENT
MEDIUMskills/pptx-posters/scripts/generate_schematic_ai.py74 # Scientific diagram best practices prompt templateCOMMENT
MEDIUMskills/treatment-plans/scripts/generate_schematic_ai.py74 # Scientific diagram best practices prompt templateCOMMENT
MEDIUM…lls/treatment-plans/scripts/validate_treatment_plan.py178 """Display comprehensive validation results."""STRING
MEDIUM…ills/statistical-analysis/scripts/assumption_checks.py186 # Levene's test (robust to non-normality)COMMENT
MEDIUM…ills/statistical-analysis/scripts/assumption_checks.py646 # Run comprehensive checkCOMMENT
MEDIUM…ls/scientific-writing/scripts/generate_schematic_ai.py74 # Scientific diagram best practices prompt templateCOMMENT
MEDIUM…ical-decision-support/scripts/generate_schematic_ai.py74 # Scientific diagram best practices prompt templateCOMMENT
MEDIUM…lls/literature-review/scripts/generate_schematic_ai.py74 # Scientific diagram best practices prompt templateCOMMENT
MEDIUM…ls/scholar-evaluation/scripts/generate_schematic_ai.py74 # Scientific diagram best practices prompt templateCOMMENT
MEDIUMskills/scholar-evaluation/scripts/calculate_scores.py149 """Generate comprehensive evaluation report."""STRING
MEDIUM…et-research-reports/scripts/generate_market_visuals.py15 # Generate all 28 visuals (for comprehensive coverage)STRING
MEDIUMskills/latex-posters/scripts/generate_schematic_ai.py74 # Scientific diagram best practices prompt templateCOMMENT
MEDIUMskills/pyopenms/scripts/accurate_mass_search.py94 # Re-read the mzTab text for a robust flat dump of the SML tableCOMMENT
MEDIUMskills/matplotlib/scripts/plot_template.py322 """Create a comprehensive figure with multiple subplots."""STRING
MEDIUMskills/venue-templates/scripts/generate_schematic_ai.py74 # Scientific diagram best practices prompt templateCOMMENT
MEDIUM…ills/clinical-reports/scripts/generate_schematic_ai.py74 # Scientific diagram best practices prompt templateCOMMENT
MEDIUMskills/clinical-reports/scripts/validate_case_report.py192 """Generate comprehensive validation report."""STRING
MEDIUM…lls/scientific-slides/scripts/generate_schematic_ai.py74 # Scientific diagram best practices prompt templateCOMMENT
MEDIUM…hypothesis-generation/scripts/generate_schematic_ai.py74 # Scientific diagram best practices prompt templateCOMMENT
MEDIUMskills/rdkit/scripts/molecular_properties.py26 """Calculate comprehensive molecular properties."""STRING
MEDIUMskills/peer-review/scripts/generate_schematic_ai.py74 # Scientific diagram best practices prompt templateCOMMENT
Over-Commented Block28 hits · 28 pts
SeverityFileLineSnippetContext
LOWskills/anndata/references/best_practices.md261 gene_expr = adata.raw[:, 'GENE_NAME'].XCOMMENT
LOWskills/exploratory-data-analysis/SKILL.md301df = pd.read_csv('experiment_results.csv')COMMENT
LOWskills/exploratory-data-analysis/SKILL.md321# 2. Read reference for ND2 formatCOMMENT
LOWskills/bids/references/conversion_tools.md361#### Step 4: ConvertCOMMENT
LOWskills/bids/references/beps.yml1---COMMENT
LOWskills/pymatgen/references/transformations_workflows.md301 relax = MPRelaxSet(slab)COMMENT
LOWskills/markitdown/SKILL.md181COMMENT
LOWskills/autoskill/config.yaml1# autoskill configurationCOMMENT
LOWskills/autoskill/references/screenpipe-config.yaml1# Starter screenpipe configuration for autoskill users.COMMENT
LOW…forecasting/examples/global-temperature/run_example.sh1#!/bin/bashCOMMENT
LOW…nical-decision-support/scripts/biomarker_classifier.py381# PT001,55.5,12.3,1+,Yes,14.2,1COMMENT
LOW…inical-decision-support/scripts/build_decision_tree.py441# Example usage:COMMENT
LOW…nical-decision-support/scripts/create_cohort_tables.py521# PT001,Biomarker+,65,Male,0-1,IV,PR,1,0,...COMMENT
LOWskills/diffdock/assets/custom_inference_config.yaml61# samples_per_complex: 30COMMENT
LOWskills/diffdock/assets/custom_inference_config.yaml81# PRESET 4: Rigid Ligands (more focused predictions)COMMENT
LOWskills/gget/references/workflows.md561 mut["pdb_id"] = NoneCOMMENT
LOWskills/literature-review/SKILL.md561 --summaryCOMMENT
LOW…ls/literature-review/references/database_strategies.md421# 2. Search bioRxivCOMMENT
LOWskills/latex-posters/SKILL.md481python scripts/generate_schematic.py "POSTER FORMAT for A0. ONE case: Company logo + 'FDA APPROVED' (150pt bold) + '2024COMMENT
LOWskills/pytorch-lightning/scripts/template_datamodule.py321 print(f"Train batches: {len(train_loader)}")COMMENT
LOWskills/stable-baselines3/scripts/evaluate_agent.py201 # Example 1: Evaluate a trained modelCOMMENT
LOWskills/stable-baselines3/scripts/evaluate_agent.py221 # watch_agent(COMMENT
LOWskills/stable-baselines3/scripts/evaluate_agent.py241 # model_path="./models/best_model/best_model.zip",COMMENT
LOWskills/stable-baselines3/scripts/train_rl_agent.py141 algorithm=PPO,COMMENT
LOWskills/stable-baselines3/scripts/train_rl_agent.py161 # algorithm=DQN,COMMENT
LOWskills/stable-baselines3/scripts/custom_env_template.py61 # 2. Multi-discrete: spaces.MultiDiscrete([n1, n2, ...])COMMENT
LOWskills/pufferlib/scripts/env_template.py41 # 'position': (2,),COMMENT
LOWskills/optimize-for-gpu/SKILL.md261# Warp (simulation, spatial computing, differentiable programming)COMMENT
Example Usage Blocks15 hits · 22 pts
SeverityFileLineSnippetContext
LOWskills/pymc/scripts/model_comparison.py360# Example usageSTRING
LOWskills/pymc/scripts/model_diagnostics.py323# Example usageCOMMENT
LOW…forecasting/examples/global-temperature/run_example.sh9# Usage:COMMENT
LOW…ills/statistical-analysis/scripts/assumption_checks.py634 # Example usageCOMMENT
LOW…decision-support/scripts/generate_survival_analysis.py413# Example usage:COMMENT
LOW…ical-decision-support/scripts/validate_cds_document.py331# Example usage:COMMENT
LOW…nical-decision-support/scripts/biomarker_classifier.py375# Example usage:COMMENT
LOW…inical-decision-support/scripts/build_decision_tree.py441# Example usage:COMMENT
LOW…nical-decision-support/scripts/create_cohort_tables.py515# Example usage:COMMENT
LOWskills/simpy/scripts/resource_monitor.py320# Example usageCOMMENT
LOWskills/pytorch-lightning/scripts/template_datamodule.py301# Example usageCOMMENT
LOW…pytorch-lightning/scripts/template_lightning_module.py198# Example usageCOMMENT
LOW…ills/scientific-visualization/scripts/figure_export.py318 # Example usageCOMMENT
LOWskills/scikit-learn/scripts/clustering_analysis.py338# Example usageCOMMENT
LOWskills/scikit-learn/scripts/classification_pipeline.py230# Example usageCOMMENT
Self-Referential Comments7 hits · 21 pts
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MEDIUMskills/open-notebook/scripts/chat_interaction.py140 # Create a notebook with some content firstCOMMENT
MEDIUMskills/open-notebook/scripts/chat_interaction.py162 # Create a chat sessionCOMMENT
MEDIUMskills/open-notebook/scripts/source_ingestion.py124 # Create a notebook firstCOMMENT
MEDIUMskills/hypogenic/references/config_template.yaml116# Define a custom function in your code to parse specific output formatsCOMMENT
MEDIUMskills/pymoo/scripts/many_objective_example.py19 # Define the problem - DTLZ2 with 5 objectivesCOMMENT
MEDIUMskills/pymoo/scripts/single_objective_example.py21 # Define the problem - Sphere function (sum of squares)COMMENT
MEDIUMskills/pymoo/scripts/multi_objective_example.py18 # Define the problem - ZDT1 (bi-objective)COMMENT
Modern Structural Boilerplate6 hits · 6 pts
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LOWskills/xlsx/scripts/office/validators/__init__.py10__all__ = [CODE
LOWskills/pptx/scripts/clean.py221def update_content_types(unpacked_dir: Path, removed_files: list[str]) -> None:CODE
LOWskills/pptx/scripts/office/validators/__init__.py10__all__ = [CODE
LOW…ills/scientific-visualization/scripts/style_presets.py195def set_color_palette(palette_name: str = 'okabe_ito') -> None:CODE
LOWskills/docx/scripts/accept_changes.py14logger = logging.getLogger(__name__)CODE
LOWskills/docx/scripts/office/validators/__init__.py10__all__ = [CODE
AI Structural Patterns5 hits · 5 pts
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LOWskills/research-lookup/scripts/research_lookup.py143CODE
LOWskills/infographics/scripts/generate_infographic_ai.py991CODE
LOW…nical-decision-support/scripts/create_cohort_tables.py419CODE
LOW…s/neuropixels-analysis/scripts/preprocess_recording.py15CODE
LOWskills/stable-baselines3/scripts/train_rl_agent.py24CODE
Fake / Example Data5 hits · 5 pts
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LOWskills/pptx-posters/assets/poster_html_template.html206 <div id="chart1" class="placeholder" style="width: 100%; height: 400pt;"></div>CODE
LOWskills/pptx-posters/assets/poster_quality_checklist.md15- [ ] No placeholder text remaining (TODO, Lorem ipsum, etc.)CODE
LOWskills/latex-posters/SKILL.md1070- [ ] No placeholder text remaining (Lorem ipsum, TODO, etc.)CODE
LOWskills/latex-posters/scripts/review_poster.sh179echo " [ ] No placeholder text (Lorem ipsum, TODO, etc.)"CODE
LOWskills/latex-posters/assets/poster_quality_checklist.md15- [ ] No placeholder text remaining (TODO, Lorem ipsum, etc.)CODE
Synthetic Comment Markers1 hit · 5 pts
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HIGHskills/latex-posters/SKILL.md114The #1 issue with AI-generated poster graphics is **TOO MUCH CONTENT**. This causes:CODE