Repository Analysis

synthetic-sciences/openscience

The open-source AI workbench for scientific research

6.9 Low AI signal View on GitHub

Analysis Overview

This report presents the forensic synthetic code analysis of synthetic-sciences/openscience, a TypeScript project with 3,355 GitHub stars. SynthScan v2.0 examined 1,054,008 lines of code across 3405 source files, recording 3849 pattern matches distributed across 25 syntactic categories. The overall adjusted score of 6.9 places this repository in the Low AI signal band.

The scanner applied 160+ deterministic lexical heuristics, multi-line block detectors, abstract syntax tree depth profilers, and a cross-file Jaccard similarity matrix to construct a statistically normalised synthetic code estimate. All matches are individually weighted by severity coefficient and contextual multiplier before summation, and the resulting headline score is temporally discounted to account for the repository's development history relative to the commercial emergence of large language model coding tooling (November 2022 onward).

6.9
Adjusted Score
6.9
Raw Score
100%
Time Factor
2026-08-29
Last Push
3.4K
Stars
TypeScript
Language
1.1M
Lines of Code
3.4K
Files
3.8K
Pattern Hits
2026-08-29
Scan Date
0.05
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

Longitudinal tracking requires multiple scan runs. Once this repository is re-scanned after new commits land, this chart will visualise how the synthetic code signal evolves over time — enabling you to detect whether AI authorship is growing, stabilising, or being actively corrected by human engineers.

No multi-scan history yet — run the scanner again to build trend data.

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 11HIGH 175MEDIUM 1186LOW 2477

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 3849 distinct pattern matches across 25 syntactic categories. Each entry below represents a discrete location in the source code where the engine recorded a statistically significant AI authorship indicator. Expand any category row to inspect the individual file paths, line numbers, code snippets, and the lexical context (CODE, COMMENT, or STRING) in which each match was detected.

Reading the findings table: The Severity column indicates the diagnostic confidence level (CRITICAL / HIGH / MEDIUM / LOW). The Context column identifies whether the match occurred inside executable code, an inline comment, or a string literal — comment-context matches receive a ×1.5 weight because LLMs systematically over-annotate. The ⚡ bolt icon marks clustered matches: three or more patterns within a 10-line window, each receiving an additional ×1.5 density multiplier as dense clusters constitute far stronger evidence of synthetic authorship than isolated hits.

Decorative Section Separators656 hits · 2050 pts
SeverityFileLineSnippetContext
MEDIUMfrontend/workspace/src/artifacts/inspector.ts134// ── Historical review records (provenance graph) ────────────────────────────COMMENT
MEDIUMfrontend/workspace/src/science/renderers/index.ts19// ── renderer registrations ─────────────────────────────────────────────────COMMENT
MEDIUMfrontend/workspace/src/science/renderers/index.ts29// ────────────────────────────────────────────────────────────────────────────COMMENT
MEDIUMfrontend/workspace/src/components/settings/_shared.tsx146// ── Toolbar pieces ──────────────────────────────────────────────────────────COMMENT
MEDIUMfrontend/workspace/src/components/settings/registry.ts4// ── Panel contract ──────────────────────────────────────────────────────────COMMENT
MEDIUMbackend/cli/test/provider/managed-routing.test.ts60// ── Pure decision helpers ────────────────────────────────────────────────────COMMENT
MEDIUMbackend/cli/test/provider/managed-routing.test.ts121// ── Availability filter (hermetic, catalog-backed) ───────────────────────────COMMENT
MEDIUMbackend/cli/test/provider/managed-routing.test.ts468// ── billing.llm gates the own-key vs managed-proxy route (1a/1b/1c) ─────────COMMENT
MEDIUMbackend/cli/test/provider/managed-routing.test.ts845// ── the invalidation must precede the announcement, not follow it ────────────COMMENT
MEDIUM…/chemistry/molecular-docking/scripts/prepare_target.py350# ---------------------------------------------------------------------------COMMENT
MEDIUM…/chemistry/molecular-docking/scripts/prepare_target.py352# ---------------------------------------------------------------------------COMMENT
MEDIUM…/chemistry/molecular-docking/scripts/prepare_target.py23# ---------------------------------------------------------------------------COMMENT
MEDIUM…/chemistry/molecular-docking/scripts/prepare_target.py25# ---------------------------------------------------------------------------COMMENT
MEDIUM…/chemistry/molecular-docking/scripts/prepare_target.py57# ---------------------------------------------------------------------------COMMENT
MEDIUM…/chemistry/molecular-docking/scripts/prepare_target.py59# ---------------------------------------------------------------------------COMMENT
MEDIUM…/chemistry/molecular-docking/scripts/prepare_target.py70# ---------------------------------------------------------------------------COMMENT
MEDIUM…/chemistry/molecular-docking/scripts/prepare_target.py72# ---------------------------------------------------------------------------COMMENT
MEDIUM…/chemistry/molecular-docking/scripts/prepare_target.py99# ---------------------------------------------------------------------------COMMENT
MEDIUM…/chemistry/molecular-docking/scripts/prepare_target.py101# ---------------------------------------------------------------------------COMMENT
MEDIUM…/chemistry/molecular-docking/scripts/prepare_target.py325# ---------------------------------------------------------------------------COMMENT
MEDIUM…/chemistry/molecular-docking/scripts/prepare_target.py327# ---------------------------------------------------------------------------COMMENT
MEDIUM…/chemistry/molecular-docking/scripts/prepare_target.py532# ---------------------------------------------------------------------------COMMENT
MEDIUM…/chemistry/molecular-docking/scripts/prepare_target.py534# ---------------------------------------------------------------------------COMMENT
MEDIUM…chemistry/molecular-docking/scripts/prepare_ligands.py23# ---------------------------------------------------------------------------COMMENT
MEDIUM…chemistry/molecular-docking/scripts/prepare_ligands.py25# ---------------------------------------------------------------------------COMMENT
MEDIUM…chemistry/molecular-docking/scripts/prepare_ligands.py42# ---------------------------------------------------------------------------COMMENT
MEDIUM…chemistry/molecular-docking/scripts/prepare_ligands.py44# ---------------------------------------------------------------------------COMMENT
MEDIUM…chemistry/molecular-docking/scripts/prepare_ligands.py250# ---------------------------------------------------------------------------COMMENT
MEDIUM…chemistry/molecular-docking/scripts/prepare_ligands.py252# ---------------------------------------------------------------------------COMMENT
MEDIUM…chemistry/molecular-docking/scripts/prepare_ligands.py355# ---------------------------------------------------------------------------COMMENT
MEDIUM…chemistry/molecular-docking/scripts/prepare_ligands.py357# ---------------------------------------------------------------------------COMMENT
MEDIUM…cli/skills/chemistry/molecular-docking/scripts/dock.py74# ---------------------------------------------------------------------------COMMENT
MEDIUM…cli/skills/chemistry/molecular-docking/scripts/dock.py76# ---------------------------------------------------------------------------COMMENT
MEDIUM…cli/skills/chemistry/molecular-docking/scripts/dock.py28# ---------------------------------------------------------------------------COMMENT
MEDIUM…cli/skills/chemistry/molecular-docking/scripts/dock.py30# ---------------------------------------------------------------------------COMMENT
MEDIUM…cli/skills/chemistry/molecular-docking/scripts/dock.py140# ---------------------------------------------------------------------------COMMENT
MEDIUM…cli/skills/chemistry/molecular-docking/scripts/dock.py142# ---------------------------------------------------------------------------COMMENT
MEDIUM…cli/skills/chemistry/molecular-docking/scripts/dock.py536# ---------------------------------------------------------------------------COMMENT
MEDIUM…cli/skills/chemistry/molecular-docking/scripts/dock.py538# ---------------------------------------------------------------------------COMMENT
MEDIUM…cli/skills/chemistry/molecular-docking/scripts/dock.py806# ---------------------------------------------------------------------------COMMENT
MEDIUM…cli/skills/chemistry/molecular-docking/scripts/dock.py808# ---------------------------------------------------------------------------COMMENT
MEDIUM…cli/skills/chemistry/molecular-docking/scripts/dock.py904# ---------------------------------------------------------------------------COMMENT
MEDIUM…cli/skills/chemistry/molecular-docking/scripts/dock.py906# ---------------------------------------------------------------------------COMMENT
MEDIUM…cli/skills/chemistry/molecular-docking/scripts/rank.py30# ---------------------------------------------------------------------------COMMENT
MEDIUM…cli/skills/chemistry/molecular-docking/scripts/rank.py32# ---------------------------------------------------------------------------COMMENT
MEDIUM…cli/skills/chemistry/molecular-docking/scripts/rank.py184# ---------------------------------------------------------------------------COMMENT
MEDIUM…cli/skills/chemistry/molecular-docking/scripts/rank.py186# ---------------------------------------------------------------------------COMMENT
MEDIUM…cli/skills/chemistry/molecular-docking/scripts/rank.py313# ---------------------------------------------------------------------------COMMENT
MEDIUM…cli/skills/chemistry/molecular-docking/scripts/rank.py315# ---------------------------------------------------------------------------COMMENT
MEDIUM…cli/skills/chemistry/molecular-docking/scripts/rank.py370# ---------------------------------------------------------------------------COMMENT
MEDIUM…cli/skills/chemistry/molecular-docking/scripts/rank.py372# ---------------------------------------------------------------------------COMMENT
MEDIUM…cli/skills/chemistry/molecular-docking/scripts/rank.py466# ---------------------------------------------------------------------------COMMENT
MEDIUM…cli/skills/chemistry/molecular-docking/scripts/rank.py468# ---------------------------------------------------------------------------COMMENT
MEDIUM…li/skills/chemistry/molecular-docking/scripts/score.py496# ---------------------------------------------------------------------------COMMENT
MEDIUM…li/skills/chemistry/molecular-docking/scripts/score.py498# ---------------------------------------------------------------------------COMMENT
MEDIUM…li/skills/chemistry/molecular-docking/scripts/score.py25# ---------------------------------------------------------------------------COMMENT
MEDIUM…li/skills/chemistry/molecular-docking/scripts/score.py27# ---------------------------------------------------------------------------COMMENT
MEDIUM…li/skills/chemistry/molecular-docking/scripts/score.py59# ---------------------------------------------------------------------------COMMENT
MEDIUM…li/skills/chemistry/molecular-docking/scripts/score.py61# ---------------------------------------------------------------------------COMMENT
MEDIUM…li/skills/chemistry/molecular-docking/scripts/score.py399# ---------------------------------------------------------------------------COMMENT
596 more matches not shown…
Structural Annotation Overuse765 hits · 1313 pts
SeverityFileLineSnippetContext
LOWbackend/cli/test/agent/harness-contract.test.ts210 expect(skill).not.toContain("### Step 5: Save Report")CODE
LOW…earch/perplexity-search/references/openrouter_setup.md19### Step 1: Create OpenRouter AccountCOMMENT
LOW…earch/perplexity-search/references/openrouter_setup.md26### Step 2: Add Payment MethodCOMMENT
LOW…earch/perplexity-search/references/openrouter_setup.md41### Step 3: Generate API KeyCOMMENT
LOW…earch/perplexity-search/references/openrouter_setup.md57### Step 4: Configure EnvironmentCOMMENT
LOW…earch/perplexity-search/references/openrouter_setup.md123### Step 5: Install DependenciesCOMMENT
LOW…earch/perplexity-search/references/openrouter_setup.md145### Step 6: Verify SetupCOMMENT
LOW…earch/perplexity-search/references/openrouter_setup.md164### Step 7: Test Your First SearchCOMMENT
LOW…lm-tools/huggingface-tokenizers/references/training.md7### Step 1: Choose tokenization algorithmCOMMENT
LOW…lm-tools/huggingface-tokenizers/references/training.md14### Step 2: Prepare training dataCOMMENT
LOW…lm-tools/huggingface-tokenizers/references/training.md37### Step 3: Initialize tokenizerCOMMENT
LOW…lm-tools/huggingface-tokenizers/references/training.md94### Step 4: TrainCOMMENT
LOW…lm-tools/huggingface-tokenizers/references/training.md114### Step 5: Add post-processingCOMMENT
LOW…lm-tools/huggingface-tokenizers/references/training.md138### Step 6: SaveCOMMENT
LOW…/skills/llm-tools/sentencepiece/references/training.md7### Step 1: Prepare corpusCOMMENT
LOW…/skills/llm-tools/sentencepiece/references/training.md19### Step 2: Train modelCOMMENT
LOW…/skills/llm-tools/sentencepiece/references/training.md45### Step 3: Load and useCOMMENT
LOW…i/skills/llm-tools/transformers/references/training.md9### Step 1: Load and Preprocess DataCOMMENT
LOW…i/skills/llm-tools/transformers/references/training.md36### Step 2: Load ModelCOMMENT
LOW…i/skills/llm-tools/transformers/references/training.md47### Step 3: Define MetricsCOMMENT
LOW…i/skills/llm-tools/transformers/references/training.md61### Step 4: Configure TrainingCOMMENT
LOW…i/skills/llm-tools/transformers/references/training.md82### Step 5: Create Trainer and TrainCOMMENT
LOW…i/skills/llm-tools/transformers/references/training.md103### Step 6: Save ModelCOMMENT
LOW…kills/llm-tools/long-context/references/fine_tuning.md488# Step 1: 2k → 8kCOMMENT
LOW…kills/llm-tools/long-context/references/fine_tuning.md491# Step 2: 8k → 16kCOMMENT
LOW…kills/llm-tools/long-context/references/fine_tuning.md494# Step 3: 16k → 32kCOMMENT
LOWbackend/cli/skills/databases/kegg-database/SKILL.md214# Step 1: Find gene ID by nameCOMMENT
LOWbackend/cli/skills/databases/kegg-database/SKILL.md217# Step 2: Link gene to pathwaysCOMMENT
LOWbackend/cli/skills/databases/kegg-database/SKILL.md220# Step 3: Get detailed pathway informationCOMMENT
LOWbackend/cli/skills/databases/kegg-database/SKILL.md235# Step 1: List all human pathwaysCOMMENT
LOWbackend/cli/skills/databases/kegg-database/SKILL.md238# Step 2: For each pathway, get associated genesCOMMENT
LOWbackend/cli/skills/databases/kegg-database/SKILL.md253# Step 1: Search for compoundCOMMENT
LOWbackend/cli/skills/databases/kegg-database/SKILL.md256# Step 2: Link compound to reactionsCOMMENT
LOWbackend/cli/skills/databases/kegg-database/SKILL.md259# Step 3: Link reactions to pathwaysCOMMENT
LOWbackend/cli/skills/databases/kegg-database/SKILL.md262# Step 4: Get pathway detailsCOMMENT
LOWbackend/cli/skills/databases/kegg-database/SKILL.md273# Step 1: Convert KEGG gene IDs to external database IDsCOMMENT
LOWbackend/cli/skills/databases/kegg-database/SKILL.md277# Step 2: Parse conversion resultsCOMMENT
LOWbackend/cli/skills/databases/kegg-database/SKILL.md283# Step 3: Get sequences using KEGGCOMMENT
LOWbackend/cli/skills/databases/kegg-database/SKILL.md294# Step 1: List pathways for multiple organismsCOMMENT
LOWbackend/cli/skills/databases/kegg-database/SKILL.md299# Step 2: Get reference pathway for comparisonCOMMENT
LOWbackend/cli/skills/databases/kegg-database/SKILL.md302# Step 3: Get organism-specific versionsCOMMENT
LOW…s/databases/cosmic-database/scripts/download_cosmic.py64 # Step 1: Get the download URLCOMMENT
LOW…s/databases/cosmic-database/scripts/download_cosmic.py91 # Step 2: Download the fileCOMMENT
LOW…s/databases/cosmic-database/scripts/download_cosmic.py99 # Step 3: Write to diskCOMMENT
LOW…skills/databases/fred-economic-data/references/tags.md411 # Step 1: Find tags matching the topicCOMMENT
LOW…skills/databases/fred-economic-data/references/tags.md428 # Step 2: Find related tagsCOMMENT
LOWbackend/cli/skills/databases/geo-database/SKILL.md261# Step 1: Search for GEO entriesCOMMENT
LOWbackend/cli/skills/databases/geo-database/SKILL.md274# Step 2: Fetch summariesCOMMENT
LOWbackend/cli/skills/databases/geo-database/SKILL.md283# Step 3: Fetch full recordsCOMMENT
LOW…databases/clinvar-database/references/api_reference.md121# Step 1: Search for variantsCOMMENT
LOW…databases/clinvar-database/references/api_reference.md124# Step 2: Parse IDs from search resultsCOMMENT
LOW…databases/clinvar-database/references/api_reference.md127# Step 3: Retrieve summariesCOMMENT
LOW…databases/clinvar-database/references/api_reference.md130# Step 4: Fetch full records if neededCOMMENT
LOW…databases/pubchem-database/references/api_reference.md154# Step 1: Submit similarity searchCOMMENT
LOW…databases/pubchem-database/references/api_reference.md161# Step 2: Check statusCOMMENT
LOW…databases/pubchem-database/references/api_reference.md164# Step 3: Poll until ready (with timeout)COMMENT
LOW…databases/pubchem-database/references/api_reference.md165# Step 4: Retrieve results from the same URLCOMMENT
LOW…atabases/pubchem-database/scripts/bioactivity_query.py307 # Step 1: Find assays for the targetCOMMENT
LOW…atabases/pubchem-database/scripts/bioactivity_query.py314 # Step 2: Get active compounds from these assaysCOMMENT
LOWbackend/cli/skills/databases/string-database/SKILL.md281# Step 1: Map gene names to STRING IDsCOMMENT
705 more matches not shown…
Excessive Try-Catch Wrapping882 hits · 1286 pts
SeverityFileLineSnippetContext
MEDIUMbackend/cli/skills/research/perplexity-search/SKILL.md211 print(f"Error: {result['error']}")CODE
LOW…skills/research/perplexity-search/scripts/setup_env.py56 except Exception as e:CODE
MEDIUM…skills/research/perplexity-search/scripts/setup_env.py57 print(f"Error creating .env file: {e}", file=sys.stderr)CODE
MEDIUM…esearch/perplexity-search/scripts/perplexity_search.py32 print("Error: LiteLLM is not installed.", file=sys.stderr)CODE
MEDIUM…esearch/perplexity-search/scripts/perplexity_search.py41 print("Error: OPENROUTER_API_KEY environment variable is not set.", file=sys.stderr)CODE
LOW…esearch/perplexity-search/scripts/perplexity_search.py126 except Exception as e:CODE
MEDIUM…esearch/perplexity-search/scripts/perplexity_search.py250 print(f"Error: {result['error']}", file=sys.stderr)STRING
LOW…cli/skills/research/research-lookup/research_lookup.py251 except Exception as e:CODE
LOW…cli/skills/research/research-lookup/research_lookup.py354 except Exception as e:CODE
MEDIUM…cli/skills/research/research-lookup/research_lookup.py391 print("Error: OPENROUTER_API_KEY environment variable not set", file=sys.stderr)CODE
MEDIUM…cli/skills/research/research-lookup/research_lookup.py413 print("Error: No query provided. Use --model-info to see available models.", file=sys.stderr)CODE
LOW…cli/skills/research/research-lookup/research_lookup.py475 except Exception as e:CODE
MEDIUM…cli/skills/research/research-lookup/research_lookup.py476 print(f"Error: {str(e)}", file=sys.stderr)CODE
LOWbackend/cli/skills/research/research-lookup/lookup.py181 except Exception as e:CODE
LOW…ls/research/research-lookup/scripts/research_lookup.py251 except Exception as e:CODE
LOW…ls/research/research-lookup/scripts/research_lookup.py354 except Exception as e:CODE
MEDIUM…ls/research/research-lookup/scripts/research_lookup.py391 print("Error: OPENROUTER_API_KEY environment variable not set", file=sys.stderr)CODE
MEDIUM…ls/research/research-lookup/scripts/research_lookup.py413 print("Error: No query provided. Use --model-info to see available models.", file=sys.stderr)CODE
LOW…ls/research/research-lookup/scripts/research_lookup.py475 except Exception as e:CODE
MEDIUM…ls/research/research-lookup/scripts/research_lookup.py476 print(f"Error: {str(e)}", file=sys.stderr)CODE
LOW…et-research-reports/scripts/generate_market_visuals.py361 except Exception as e:CODE
LOW…ualization/scientific-schematics/test_ai_generation.py76 except Exception as e:CODE
LOW…ualization/scientific-schematics/test_ai_generation.py109 except Exception as e:CODE
LOW…ualization/scientific-schematics/test_ai_generation.py129 except Exception as e:CODE
LOW…ualization/scientific-schematics/test_ai_generation.py168 except Exception as e:CODE
LOW…ualization/scientific-schematics/test_ai_generation.py212 except Exception as e:CODE
MEDIUM…scientific-schematics/scripts/generate_schematic_ai.py34 print("Error: requests library not found. Install with: pip install requests")CODE
LOW…scientific-schematics/scripts/generate_schematic_ai.py324 except Exception as e:CODE
LOW…scientific-schematics/scripts/generate_schematic_ai.py417 except Exception as e:CODE
LOW…scientific-schematics/scripts/generate_schematic_ai.py588 except Exception as e:CODE
MEDIUM…scientific-schematics/scripts/generate_schematic_ai.py821 print("Error: Iterations must be between 1 and 2")STRING
LOW…scientific-schematics/scripts/generate_schematic_ai.py840 except Exception as e:STRING
MEDIUM…on/scientific-schematics/scripts/generate_schematic.py99 print(f"Error: AI generation script not found: {ai_script}")STRING
LOW…on/scientific-schematics/scripts/generate_schematic.py123 except Exception as e:STRING
MEDIUM…on/scientific-schematics/scripts/generate_schematic.py124 print(f"Error executing AI generation: {e}")STRING
MEDIUM…ualization/protein-diagram/scripts/draw_contact_map.py20 print("Error: BioPython is required. Install with: pip install biopython", file=sys.stderr)CODE
MEDIUM…ualization/protein-diagram/scripts/draw_contact_map.py75 print(f"Error: No C-alpha atoms found for chain {args.chain}.", file=sys.stderr)CODE
MEDIUM…isualization/protein-diagram/scripts/draw_alignment.py20 print("Error: pyMSAviz is required. Install with: pip install pymsaviz", file=sys.stderr)CODE
MEDIUM…on/protein-diagram/scripts/draw_secondary_structure.py20 print("Error: BioPython is required. Install with: pip install biopython", file=sys.stderr)CODE
LOW…on/protein-diagram/scripts/draw_secondary_structure.py55 except Exception:CODE
LOW…on/protein-diagram/scripts/draw_secondary_structure.py58 except Exception as e:CODE
MEDIUM…on/protein-diagram/scripts/draw_secondary_structure.py59 print(f"Error running DSSP: {e}", file=sys.stderr)CODE
MEDIUM…on/protein-diagram/scripts/draw_secondary_structure.py78 print("Error: No residues found for specified chain.", file=sys.stderr)CODE
MEDIUM…visualization/protein-diagram/scripts/draw_features.py52 print(f"Error fetching UniProt data for {uniprot_id}: {e}", file=sys.stderr)CODE
MEDIUM…visualization/protein-diagram/scripts/draw_features.py92 print(f"Error: Cannot parse features from '{features_arg}'.", file=sys.stderr)CODE
MEDIUM…visualization/protein-diagram/scripts/draw_features.py123 print("Error: Provide either --uniprot or --features.", file=sys.stderr)CODE
MEDIUM…sualization/protein-diagram/scripts/draw_domain_map.py41 print(f"Error fetching InterPro data for {uniprot_id}: {e}", file=sys.stderr)CODE
LOW…sualization/protein-diagram/scripts/draw_domain_map.py51 except Exception:CODE
MEDIUM…sualization/protein-diagram/scripts/draw_domain_map.py84 print(f"Error: Cannot parse domains from '{domains_arg}'. Provide a JSON file or inline JSON array.",CODE
MEDIUM…sualization/protein-diagram/scripts/draw_domain_map.py171 print("Error: Could not determine protein length. Provide --length.", file=sys.stderr)CODE
MEDIUM…sualization/protein-diagram/scripts/draw_domain_map.py181 print("Error: Provide either --uniprot or --domains.", file=sys.stderr)CODE
MEDIUM…alization/protein-diagram/scripts/draw_ramachandran.py22 print("Error: BioPython is required. Install with: pip install biopython", file=sys.stderr)CODE
MEDIUM…alization/protein-diagram/scripts/draw_ramachandran.py95 print("Error: No phi/psi angles found. Check PDB file and chain ID.", file=sys.stderr)CODE
MEDIUM…zation/infographics/scripts/generate_infographic_ai.py35 print("Error: requests library not found. Install with: pip install requests")CODE
LOW…zation/infographics/scripts/generate_infographic_ai.py286 except Exception:STRING
LOW…zation/infographics/scripts/generate_infographic_ai.py504 except Exception as e:CODE
LOW…zation/infographics/scripts/generate_infographic_ai.py578 except Exception as e:CODE
LOW…zation/infographics/scripts/generate_infographic_ai.py706 except Exception as e:CODE
LOW…zation/infographics/scripts/generate_infographic_ai.py808 except Exception as e:CODE
LOW…zation/infographics/scripts/generate_infographic_ai.py959 except Exception as e:CODE
822 more matches not shown…
Magic Placeholder Names89 hits · 480 pts
SeverityFileLineSnippetContext
HIGH…esearch/perplexity-search/scripts/perplexity_search.py45 print(" export OPENROUTER_API_KEY='your-api-key-here'", file=sys.stderr)CODE
HIGH…esearch/perplexity-search/scripts/perplexity_search.py47 print(" OPENROUTER_API_KEY=your-api-key-here", file=sys.stderr)CODE
HIGH…zation/infographics/scripts/generate_infographic_ai.py1284 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGH…alization/infographics/scripts/generate_infographic.py182 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGHbackend/cli/skills/llm-tools/dspy/SKILL.md293 api_key="your-api-key", # Or set ANTHROPIC_API_KEY env varCODE
HIGHbackend/cli/skills/llm-tools/dspy/SKILL.md305 api_key="your-api-key",CODE
HIGHbackend/cli/skills/llm-tools/langsmith/SKILL.md46export LANGSMITH_API_KEY="your-api-key"CODE
HIGH…ills/llm-tools/langsmith/references/troubleshooting.md45export LANGSMITH_API_KEY="your-api-key"CODE
HIGH…ills/llm-tools/langsmith/references/troubleshooting.md48LANGSMITH_API_KEY=your-api-keyCODE
HIGH…ills/llm-tools/langsmith/references/troubleshooting.md55client = Client(api_key="your-api-key")CODE
HIGHbackend/cli/skills/llm-tools/langchain/SKILL.md340os.environ["LANGCHAIN_API_KEY"] = "your-api-key"CODE
HIGH…i/skills/llm-tools/langchain/references/integration.md40pinecone.init(api_key="your-api-key", environment="us-west1-gcp")CODE
HIGHbackend/cli/skills/llm-tools/guidance/SKILL.md273 api_key="your-api-key" # Or set ANTHROPIC_API_KEY env varCODE
HIGHbackend/cli/skills/llm-tools/guidance/SKILL.md282 api_key="your-api-key" # Or set OPENAI_API_KEY env varCODE
HIGH…d/cli/skills/llm-tools/guidance/references/backends.md28 api_key="your-api-key-here"CODE
HIGH…d/cli/skills/llm-tools/guidance/references/backends.md53 api_key="your-api-key",CODE
HIGH…d/cli/skills/llm-tools/guidance/references/backends.md95 api_key="your-api-key-here"CODE
HIGH…d/cli/skills/llm-tools/guidance/references/backends.md120 api_key="your-api-key",CODE
HIGHbackend/cli/skills/llm-tools/pinecone/SKILL.md51pc = Pinecone(api_key="your-api-key")CODE
HIGHbackend/cli/skills/llm-tools/qdrant/SKILL.md419 api_key="your-api-key"CODE
HIGH…/skills/llm-tools/qdrant/references/troubleshooting.md117 api_key="your-api-key"CODE
HIGH…lls/llm-tools/generate-image/scripts/generate_image.py125 print("or set it for this run: export OPENROUTER_API_KEY=your-api-key-here.")CODE
HIGHbackend/cli/skills/llm-tools/outlines/SKILL.md225 api_key="your-api-key"CODE
HIGH…d/cli/skills/llm-tools/outlines/references/backends.md381model = outlines.models.openai("gpt-4o-mini", api_key="your-api-key")CODE
HIGH…d/cli/skills/llm-tools/outlines/references/backends.md393 api_key="your-api-key", # Or set OPENAI_API_KEY env varCODE
HIGHbackend/cli/skills/llm-tools/instructor/SKILL.md342 Anthropic(api_key="your-api-key")CODE
HIGHbackend/cli/skills/llm-tools/instructor/SKILL.md360 OpenAI(api_key="your-api-key")CODE
HIGH…li/skills/llm-tools/instructor/references/providers.md16 Anthropic(api_key="your-api-key")CODE
HIGHbackend/cli/skills/databases/uspto-database/SKILL.md156 "X-Api-Key": "YOUR_API_KEY",CODE
HIGH…s/databases/uspto-database/references/trademark_api.md26X-Api-Key: YOUR_API_KEYCODE
HIGH…s/databases/uspto-database/references/trademark_api.md123data = get_trademark_status("87654321", "YOUR_API_KEY")CODE
HIGH…s/databases/uspto-database/references/trademark_api.md147X-Api-Key: YOUR_API_KEYCODE
HIGH…s/databases/uspto-database/references/trademark_api.md240xml_data = search_trademark_assignments("5678901", "YOUR_API_KEY")CODE
HIGH…atabases/uspto-database/references/patentsearch_api.md14X-Api-Key: YOUR_API_KEYCODE
HIGH…atabases/uspto-database/references/patentsearch_api.md177 -H "X-Api-Key: YOUR_API_KEY" \CODE
HIGH…atabases/uspto-database/references/patentsearch_api.md199 "X-Api-Key": "YOUR_API_KEY",CODE
HIGH…ls/databases/gene-database/references/api_reference.md191api-key: YOUR_API_KEYCODE
HIGH…/databases/drugbank-database/references/data-access.md149headers = {"Authorization": "Bearer YOUR_API_KEY"}CODE
HIGHbackend/cli/skills/databases/fda-database/SKILL.md45fda = FDAQuery(api_key="YOUR_API_KEY")CODE
HIGH…databases/fda-database/references/animal_veterinary.md93api_key = "YOUR_API_KEY"CODE
HIGH…li/skills/databases/fda-database/references/devices.md53api_key = "YOUR_API_KEY"CODE
HIGH…/cli/skills/databases/fda-database/references/foods.md54api_key = "YOUR_API_KEY"CODE
HIGH…/cli/skills/databases/fda-database/references/drugs.md39api_key = "YOUR_API_KEY"CODE
HIGH…/cli/skills/databases/fda-database/references/other.md81api_key = "YOUR_API_KEY"CODE
HIGH…cli/skills/databases/fda-database/scripts/fda_query.py11 fda = FDAQuery(api_key="YOUR_API_KEY")STRING
HIGHbackend/cli/skills/databases/pubmed-database/SKILL.md136 "api_key": "YOUR_API_KEY" # Optional but recommendedCODE
HIGHbackend/cli/skills/databases/pubmed-database/SKILL.md148 "api_key": "YOUR_API_KEY"CODE
HIGH…/databases/pubmed-database/references/api_reference.md17esearch.fcgi?db=pubmed&term=cancer&api_key=YOUR_API_KEYCODE
HIGH…/databases/pubmed-database/references/api_reference.md51esearch.fcgi?db=pubmed&term=breast+cancer&retmax=100&retmode=json&api_key=YOUR_API_KEYCODE
HIGH…/databases/pubmed-database/references/api_reference.md80efetch.fcgi?db=pubmed&id=123456,234567&rettype=abstract&retmode=text&api_key=YOUR_API_KEYCODE
HIGH…/databases/pubmed-database/references/api_reference.md105esummary.fcgi?db=pubmed&id=123456,234567&retmode=json&version=2.0&api_key=YOUR_API_KEYCODE
HIGH…/databases/pubmed-database/references/api_reference.md129epost.fcgi?db=pubmed&id=123456,234567,345678&api_key=YOUR_API_KEYCODE
HIGH…/databases/pubmed-database/references/api_reference.md154elink.fcgi?dbfrom=pubmed&db=pubmed&id=123456&cmd=neighbor&api_key=YOUR_API_KEYCODE
HIGH…/databases/pubmed-database/references/api_reference.md175einfo.fcgi?db=pubmed&retmode=json&api_key=YOUR_API_KEYCODE
HIGH…/databases/pubmed-database/references/api_reference.md195egquery.fcgi?term=cancer&api_key=YOUR_API_KEYCODE
HIGH…/databases/pubmed-database/references/api_reference.md210espell.fcgi?db=pubmed&term=cancre&api_key=YOUR_API_KEYCODE
HIGH…/databases/pubmed-database/references/api_reference.md242esearch.fcgi?db=pubmed&term=cancer&usehistory=y&retmode=json&api_key=YOUR_API_KEYCODE
HIGH…/databases/pubmed-database/references/api_reference.md247efetch.fcgi?db=pubmed&query_key=1&WebEnv=MCID_12345&retstart=0&retmax=500&rettype=xml&api_key=YOUR_API_KEYCODE
HIGH…/databases/pubmed-database/references/api_reference.md248efetch.fcgi?db=pubmed&query_key=1&WebEnv=MCID_12345&retstart=500&retmax=500&rettype=xml&api_key=YOUR_API_KEYCODE
HIGH…/databases/pubmed-database/references/api_reference.md257epost.fcgi?db=pubmed&id=123,456,789,...&api_key=YOUR_API_KEYCODE
29 more matches not shown…
Hyper-Verbose Identifiers421 hits · 420 pts
SeverityFileLineSnippetContext
LOWtooling/repo/npm-release.ts119export function nativeReleasePackageNames() {CODE
LOWtooling/repo/npm-release.ts201export function createCompiledPackageManifest(CODE
LOWtooling/repo/npm-release.ts363export async function verifyPackedModuleExports(CODE
LOWtooling/repo/npm-release.ts524export async function verifyPublishedPackageIntegrities(inputs: PackedPackage[], options: NpmCommandOptions = {}) {CODE
LOWtooling/repo/npm-release.ts531async function submitCandidatePackageOnce(CODE
LOWtooling/repo/npm-release.ts574export async function assertReleaseVersionUnoccupied(version: string, options: NpmCommandOptions = {}) {CODE
LOWtooling/repo/npm-release.ts596export async function verifyReleaseOptionalDependencies(artifacts: PackedPackage[], options: NpmCommandOptions = {}) {CODE
LOWevals/cadence-harness/tree-metrics.ts98export function aggregateCapturedSessionTree(CODE
LOWfrontend/ui/src/context/marked.tsx403export function registerOpenScienceDiffTheme(diffs: Pick<DiffsModule, "registerCustomTheme">) {CODE
LOWfrontend/ui/src/components/dropdown-menu.tsx182function DropdownMenuItemDescription(props: ParentProps<DropdownMenuItemDescriptionProps>) {CODE
LOWfrontend/ui/src/components/dropdown-menu.tsx198function DropdownMenuItemIndicator(props: ParentProps<DropdownMenuItemIndicatorProps>) {CODE
LOWfrontend/ui/src/theme/resolve.ts300function generateNeutralAlphaScale(neutralScale: HexColor[], isDark: boolean): HexColor[] {CODE
LOWfrontend/workspace/script/e2e-mode.ts62export function externalRunnerEnvironment(env: Environment, packaged = false): Record<string, string> {CODE
LOWfrontend/workspace/src/artifacts/bytes.ts15export function storedArtifactPreviewKind(version: StoredArtifactVersion): StoredArtifactPreview["kind"] | undefined {CODE
LOWfrontend/workspace/src/artifacts/bytes.ts51export async function loadStoredArtifactPreview(CODE
LOW…ontend/workspace/src/artifacts/stored-artifact-menu.ts3export function moveStoredArtifactMenuFocus(scope: HTMLElement, target: EventTarget | null, key: string) {CODE
LOWfrontend/workspace/src/artifacts/inspector.ts158export function normalizeHistoricalReviews(value: unknown): HistoricalReviewFinding[] {CODE
LOWfrontend/workspace/src/artifacts/inspector.ts351export function normalizePublicationReview(format: string, value: unknown): PublicationReviewState {CODE
LOWfrontend/workspace/src/artifacts/store.ts74export function normalizeStoredArtifactVersion(value: unknown): StoredArtifactVersion | undefined {CODE
LOWfrontend/workspace/src/artifacts/store.ts108export function storedArtifactReviewTargetID(version: Pick<StoredArtifactVersion, "id" | "sha256">) {CODE
LOWfrontend/workspace/src/artifacts/store.ts154export function normalizeStoredArtifactDetail(value: unknown): StoredArtifactDetail | undefined {CODE
LOWfrontend/workspace/src/context/session-hydration.ts54export function nextReconnectHydrationLimit(input: { limit: number; snapshotCount: number; overlapsCached: boolean }) {CODE
LOWfrontend/workspace/src/context/session-hydration.ts60export function createReconnectGenerationGuard() {CODE
LOWfrontend/workspace/src/context/terminal.tsx29function createProjectTerminalSession(CODE
LOWfrontend/workspace/src/context/permission.tsx40function hasAutoAcceptPermissionConfig(permission: unknown) {CODE
LOWfrontend/workspace/src/science/formats/binary.ts33export function detectBinaryScienceFormat(extension: string): BinaryScienceFormat | undefined {CODE
LOWfrontend/workspace/src/utils/stale-build-recovery.ts20export function installStaleBuildRecovery(options: StaleBuildRecoveryOptions = {}): () => void {CODE
LOWfrontend/workspace/src/utils/native-picker.ts18export async function openNativeDirectoryPicker(CODE
LOW…ontend/workspace/src/components/prompt-capabilities.ts62export function publishCapabilityPreferences(preferences: CapabilityPreferences) {CODE
LOWfrontend/workspace/src/components/prompt-submission.ts8export function canRestoreFailedSubmission(current: Prompt, mode: "normal" | "shell") {CODE
LOW…nd/workspace/src/components/model-settings-popover.tsx55export function modelRadioNavigationTarget(scope: HTMLElement, target: EventTarget | null, key: string) {CODE
LOW…pace/src/components/settings/scientific-tools-state.ts78export function filterScientificCapabilities(CODE
LOW…nd/workspace/src/components/settings/connector-form.ts71export function connectorMatchesCatalogSetup(CODE
LOWfrontend/workspace/src/atlas/skill-permissions.ts54export function restoreExactSkillPermission(current: unknown, before: unknown, name: string) {CODE
LOWfrontend/workspace/src/atlas/file-viewer.ts78export function isFileRequestCancellation(error: unknown) {CODE
LOWfrontend/workspace/src/atlas/kernel-api.ts57export function createKernelRouteRequester(request: KernelTransport) {CODE
LOWfrontend/workspace/src/atlas/file-sources.ts158export function connectedFilesystemGrants(snapshot?: FilesystemSnapshot) {CODE
LOW…pace/src/atlas/project-workspace-lifecycle.fixture.tsx5export function mountProjectWorkspaceLifecycle(host: HTMLElement) {CODE
LOWfrontend/workspace/src/atlas/terminal-endpoint.ts3export function terminalEndpointAvailable(value: string, origin?: string) {CODE
LOWfrontend/workspace/src/atlas/session-trace-model.ts163export function fallbackObservableKernels(CODE
LOWfrontend/workspace/src/atlas/ExecutionHistoryAPI.ts91export function createExecutionHistoryAPI(request: RequestTransport) {CODE
LOWfrontend/workspace/src/atlas/execution-authority.ts71export function createExecutionAuthorityAPI(request: ProjectRequest) {CODE
LOWfrontend/workspace/src/atlas/execution-authority.ts117export function executionAuthorityMessage(decision: ExecutionDecision): string | undefined {CODE
LOWbackend/cli/script/encrypt-prompts-plugin.ts25export function createEncryptPromptsPlugin(keyFragments: string[]): {CODE
LOWbackend/cli/script/publish-manifest.ts28export function assertPublicPackageSurface(files: Record<string, string>) {CODE
LOWbackend/cli/script/publish-manifest.ts37export function createWrapperPackageManifest(options: WrapperPackageManifestOptions) {CODE
LOW…cli/skills/research/research-lookup/research_lookup.py300 def _extract_citations_from_text(self, text: str) -> List[Dict[str, str]]:CODE
LOWbackend/cli/skills/research/research-lookup/examples.py17def example_automatic_selection():CODE
LOWbackend/cli/skills/research/research-lookup/examples.py97def example_scientific_writing_workflow():CODE
LOW…ls/research/research-lookup/scripts/research_lookup.py300 def _extract_citations_from_text(self, text: str) -> List[Dict[str, str]]:CODE
LOW…scientific-schematics/scripts/generate_schematic_ai.py249 def _extract_image_from_response(self, response: Dict[str, Any]) -> Optional[bytes]:CODE
LOW…zation/infographics/scripts/generate_infographic_ai.py582 def _enhance_prompt_with_research(self, user_prompt: str, research_data: Dict[str, Any]) -> str:CODE
LOW…zation/infographics/scripts/generate_infographic_ai.py652 def _extract_image_from_response(self, response: Dict[str, Any]) -> Optional[bytes]:CODE
LOW…ills/visualization/matplotlib/scripts/plot_template.py316def create_comprehensive_figure():CODE
LOWbackend/cli/skills/llm-tools/nemo-guardrails/SKILL.md97async def check_output_hallucination(context):CODE
LOW…i/skills/llm-tools/instructor/references/validation.md295 def at_least_one_high_priority(cls, v):CODE
LOW…d/cli/skills/llm-tools/long-context/references/rope.md114def apply_rotary_pos_emb_gpt_neox(q, k, cos, sin, position_ids=None):CODE
LOW…llm-tools/long-context/references/extension_methods.md48def yarn_find_correction_range(low_rot, high_rot, dim, base=10000, max_position_embeddings=2048):CODE
LOW…kills/llm-tools/long-context/references/fine_tuning.md226def prepare_long_context_data(dataset, tokenizer, context_length=32768):CODE
LOWbackend/cli/skills/databases/uspto-database/SKILL.md502def comprehensive_patent_analysis(patent_number, api_key):CODE
361 more matches not shown…
Modern AI Meta-Vocabulary93 hits · 269 pts
SeverityFileLineSnippetContext
MEDIUMfrontend/landing/public/docs/assets/index-Cazmh0hf.js300`,T1='---\ntitle: "Local models"\ndescription: "Run OpenScience against a local LLM — Ollama, LM Studio, llama.cpp, vLLMCODE
MEDIUMbackend/cli/AGENTS.md26### RAG & RetrievalCOMMENT
MEDIUMbackend/cli/skills/llm-tools/dspy/SKILL.md252#### RAG System with OptimizationCOMMENT
MEDIUM…ckend/cli/skills/llm-tools/dspy/references/examples.md12## RAG SystemsCOMMENT
MEDIUM…ckend/cli/skills/llm-tools/dspy/references/examples.md14### Basic RAGCOMMENT
MEDIUM…ckend/cli/skills/llm-tools/dspy/references/examples.md40# Use RAGCOMMENT
MEDIUM…ckend/cli/skills/llm-tools/dspy/references/examples.md46### Optimized RAGCOMMENT
MEDIUM…ckend/cli/skills/llm-tools/dspy/references/examples.md65# Optimize RAGCOMMENT
MEDIUM…ckend/cli/skills/llm-tools/dspy/references/examples.md69# Optimized RAG performs better on similar questionsCOMMENT
MEDIUM…ckend/cli/skills/llm-tools/dspy/references/examples.md73### Multi-Hop RAGCOMMENT
MEDIUM…ckend/cli/skills/llm-tools/dspy/references/examples.md105# Use multi-hop RAGCOMMENT
MEDIUM…ckend/cli/skills/llm-tools/dspy/references/examples.md112### RAG with RerankingCOMMENT
MEDIUM…ckend/cli/skills/llm-tools/dspy/references/examples.md225# Use multi-agent systemCOMMENT
MEDIUM…end/cli/skills/llm-tools/dspy/references/optimizers.md71# Now optimized_qa has learned few-shot examples!COMMENT
MEDIUM…end/cli/skills/llm-tools/dspy/references/optimizers.md433# Stage 1: Bootstrap few-shotCOMMENT
MEDIUMbackend/cli/skills/llm-tools/nemo-guardrails/SKILL.md291- Docs: https://docs.nvidia.com/nemo/guardrails/STRING
MEDIUMbackend/cli/skills/llm-tools/llamaindex/SKILL.md53### 5-line RAG exampleCOMMENT
MEDIUMbackend/cli/skills/llm-tools/llamaindex/SKILL.md194### RAG agent (document search + tools)COMMENT
MEDIUMbackend/cli/skills/llm-tools/llamaindex/SKILL.md219## Advanced RAG patternsCOMMENT
MEDIUMbackend/cli/skills/llm-tools/llamaindex/SKILL.md422## Multi-modal RAGCOMMENT
MEDIUMbackend/cli/skills/llm-tools/llamaindex/SKILL.md461# Evaluate faithfulness (no hallucination)COMMENT
MEDIUMbackend/cli/skills/llm-tools/llamaindex/SKILL.md488# Complete RAG pipelineCOMMENT
MEDIUM…kills/llm-tools/llamaindex/references/query_engines.md34# Combines chunks that fit in context windowCOMMENT
MEDIUM…kills/llm-tools/llamaindex/references/query_engines.md297# 2. context - Simple RAGCOMMENT
MEDIUM…d/cli/skills/llm-tools/llamaindex/references/agents.md25## RAG agentCOMMENT
MEDIUM…d/cli/skills/llm-tools/llamaindex/references/agents.md39# Agent with RAG + calculatorCOMMENT
MEDIUMbackend/cli/skills/llm-tools/crewai/SKILL.md375## Flows - Event-driven orchestrationCOMMENT
MEDIUM…/skills/llm-tools/blip-2/references/troubleshooting.md354### VQA hallucinationsCOMMENT
MEDIUMbackend/cli/skills/llm-tools/langchain/SKILL.md12# LangChain - Build LLM Applications with Agents & RAGCOMMENT
MEDIUMbackend/cli/skills/llm-tools/langchain/SKILL.md184## RAG (Retrieval-Augmented Generation)COMMENT
MEDIUMbackend/cli/skills/llm-tools/langchain/SKILL.md186### Basic RAG pipelineCOMMENT
MEDIUMbackend/cli/skills/llm-tools/langchain/SKILL.md228### Conversational RAG with memoryCOMMENT
MEDIUMbackend/cli/skills/llm-tools/langchain/SKILL.md233# RAG with conversation memoryCOMMENT
MEDIUMbackend/cli/skills/llm-tools/langchain/SKILL.md243# Multi-turn RAGCOMMENT
MEDIUM…ckend/cli/skills/llm-tools/langchain/references/rag.md1# LangChain RAG GuideCOMMENT
MEDIUM…ckend/cli/skills/llm-tools/langchain/references/rag.md5## What is RAG?COMMENT
MEDIUM…ckend/cli/skills/llm-tools/langchain/references/rag.md17## RAG pipeline componentsCOMMENT
MEDIUM…ckend/cli/skills/llm-tools/langchain/references/rag.md194## Advanced RAG patternsCOMMENT
MEDIUM…ckend/cli/skills/llm-tools/langchain/references/rag.md196### Conversational RAGCOMMENT
MEDIUM…ckend/cli/skills/llm-tools/langchain/references/rag.md209# Conversational RAG chainCOMMENT
MEDIUM…ckend/cli/skills/llm-tools/langchain/references/rag.md341## RAG with agentsCOMMENT
MEDIUM…ckend/cli/skills/llm-tools/langchain/references/rag.md343### Agent-based RAGCOMMENT
MEDIUM…ckend/cli/skills/llm-tools/langchain/references/rag.md582# Async RAG for concurrent queriesCOMMENT
MEDIUM…nd/cli/skills/llm-tools/langchain/references/agents.md160### 2. ReAct agent (reasoning trace)COMMENT
MEDIUM…d/cli/skills/llm-tools/guidance/references/backends.md415# - Avoid large few-shot examplesCOMMENT
MEDIUMbackend/cli/skills/llm-tools/qdrant/SKILL.md230## RAG integrationCOMMENT
MEDIUMbackend/cli/skills/llm-tools/qdrant/SKILL.md265# RAG retrievalCOMMENT
MEDIUMbackend/cli/skills/llm-tools/qdrant/SKILL.md275# Use in RAG pipelineCOMMENT
MEDIUMbackend/cli/skills/llm-tools/whisper/SKILL.md244# Use transcription in RAGCOMMENT
MEDIUMbackend/cli/skills/chemistry/molfeat/SKILL.md154# MACCS - Fast, good for scaffold hoppingCOMMENT
MEDIUMbackend/cli/skills/chemistry/molfeat/SKILL.md209# MACCS - Fast, scaffold-based similarityCOMMENT
MEDIUM…/skills/chemistry/pytdc/scripts/load_and_split_data.py196 # Example 1: Single prediction with scaffold splitCOMMENT
MEDIUMbackend/cli/skills/chemistry/datamol/SKILL.md263# Get Bemis-Murcko scaffold (core structure)COMMENT
MEDIUMbackend/cli/skills/chemistry/datamol/SKILL.md270# Group compounds by scaffoldCOMMENT
MEDIUMbackend/cli/skills/chemistry/datamol/SKILL.md276# Count scaffold frequencyCOMMENT
MEDIUMbackend/cli/skills/chemistry/datamol/SKILL.md280# Create scaffold-to-molecules mappingCOMMENT
MEDIUMbackend/cli/skills/chemistry/datamol/SKILL.md545# Group by scaffoldCOMMENT
MEDIUMbackend/cli/skills/chemistry/datamol/SKILL.md556# Analyze each scaffold seriesCOMMENT
MEDIUM…ls/chemistry/datamol/references/fragments_scaffolds.md3## Scaffolds Module (`datamol.scaffold`)COMMENT
MEDIUM…ls/chemistry/datamol/references/fragments_scaffolds.md28# Count scaffold frequencyCOMMENT
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Deep Nesting284 hits · 253 pts
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LOW…cli/skills/research/research-lookup/research_lookup.py358CODE
LOW…ls/research/research-lookup/scripts/research_lookup.py358CODE
LOW…scientific-schematics/scripts/generate_schematic_ai.py249CODE
LOW…scientific-schematics/scripts/generate_schematic_ai.py358CODE
LOW…scientific-schematics/scripts/generate_schematic_ai.py451CODE
LOW…visualization/protein-diagram/scripts/draw_features.py96CODE
LOW…sualization/protein-diagram/scripts/draw_domain_map.py34CODE
LOW…alization/protein-diagram/scripts/draw_ramachandran.py31CODE
LOW…zation/infographics/scripts/generate_infographic_ai.py398CODE
LOW…zation/infographics/scripts/generate_infographic_ai.py652CODE
LOW…zation/infographics/scripts/generate_infographic_ai.py813CODE
LOW…visualization/matplotlib/scripts/style_configurator.py196CODE
LOW…visualization/matplotlib/scripts/style_configurator.py277CODE
LOW…tion/scientific-visualization/scripts/style_presets.py111CODE
LOW…lls/llm-tools/generate-image/scripts/generate_image.py23CODE
LOW…lls/llm-tools/generate-image/scripts/generate_image.py87CODE
LOW…ills/databases/uspto-database/scripts/patent_search.py252CODE
LOW…s/databases/uspto-database/scripts/trademark_client.py226CODE
LOW…s/databases/uspto-database/scripts/trademark_client.py183CODE
LOW…skills/databases/uspto-database/scripts/peds_client.py214CODE
LOW…skills/databases/uspto-database/scripts/peds_client.py155CODE
LOW…s/databases/cosmic-database/scripts/download_cosmic.py30CODE
LOW…s/databases/gene-database/scripts/batch_gene_lookup.py96CODE
LOW…s/databases/gene-database/scripts/batch_gene_lookup.py182CODE
LOW…lls/databases/gene-database/scripts/fetch_gene_data.py157CODE
LOW…s/databases/biorxiv-database/scripts/biorxiv_search.py301CODE
LOW…atabases/pubchem-database/scripts/bioactivity_query.py255CODE
LOW…databases/drugbank-database/scripts/drugbank_helper.py277CODE
LOW…ases/brenda-database/scripts/enzyme_pathway_builder.py180CODE
LOW…ases/brenda-database/scripts/enzyme_pathway_builder.py274CODE
LOW…ases/brenda-database/scripts/enzyme_pathway_builder.py348CODE
LOW…ases/brenda-database/scripts/enzyme_pathway_builder.py450CODE
LOW…ases/brenda-database/scripts/enzyme_pathway_builder.py596CODE
LOW…ases/brenda-database/scripts/enzyme_pathway_builder.py696CODE
LOW…ases/brenda-database/scripts/enzyme_pathway_builder.py805CODE
LOW…ases/brenda-database/scripts/enzyme_pathway_builder.py463CODE
LOW…/skills/databases/fda-database/scripts/fda_examples.py144CODE
LOW…/skills/databases/fda-database/scripts/fda_examples.py252CODE
LOW…cli/skills/databases/fda-database/scripts/fda_query.py108CODE
LOW…ls/databases/ensembl-database/scripts/ensembl_query.py314CODE
LOW…ls/databases/ensembl-database/scripts/ensembl_query.py50CODE
LOW…ls/databases/clinpgx-database/scripts/query_clinpgx.py41CODE
LOW…s/databases/uniprot-database/scripts/uniprot_client.py233CODE
LOW…/databases/reactome-database/scripts/reactome_query.py241CODE
LOW…databases/openalex-database/scripts/openalex_client.py44CODE
LOW…databases/openalex-database/scripts/openalex_client.py238CODE
LOW…i/skills/chemistry/medchem/scripts/filter_molecules.py32CODE
LOW…i/skills/chemistry/medchem/scripts/filter_molecules.py114CODE
LOW…i/skills/chemistry/medchem/scripts/filter_molecules.py205CODE
LOW…/chemistry/molecular-docking/scripts/prepare_target.py104CODE
LOW…/chemistry/molecular-docking/scripts/prepare_target.py121CODE
LOW…/chemistry/molecular-docking/scripts/prepare_target.py162CODE
LOW…/chemistry/molecular-docking/scripts/prepare_target.py286CODE
LOW…/chemistry/molecular-docking/scripts/prepare_target.py355CODE
LOW…chemistry/molecular-docking/scripts/prepare_ligands.py47CODE
LOW…chemistry/molecular-docking/scripts/prepare_ligands.py155CODE
LOW…chemistry/molecular-docking/scripts/prepare_ligands.py186CODE
LOW…chemistry/molecular-docking/scripts/prepare_ligands.py255CODE
LOW…cli/skills/chemistry/molecular-docking/scripts/dock.py159CODE
LOW…cli/skills/chemistry/molecular-docking/scripts/dock.py242CODE
224 more matches not shown…
Cross-Language Confusion (JS/TS)35 hits · 205 pts
SeverityFileLineSnippetContext
HIGH…nd/cli/test/skill/image-generation-entrypoints.test.ts49print(json.dumps({CODE
HIGH…nd/cli/test/skill/image-generation-entrypoints.test.ts91print(json.dumps(errors))CODE
HIGHbackend/cli/src/file/science.ts51 print(json.dumps({"error": "h5py is not available", "detail": str(exc)}))CODE
HIGHbackend/cli/src/file/science.ts172print(json.dumps(result))CODE
HIGHbackend/cli/src/cli/ui.ts61 print(...message)CODE
HIGHbackend/cli/src/compute/ssh/adapter.ts298 return FalseCODE
HIGHbackend/cli/src/compute/ssh/adapter.ts304 return FalseCODE
HIGHbackend/cli/src/compute/ssh/adapter.ts306 return TrueCODE
HIGHbackend/cli/src/compute/ssh/adapter.ts344 return FalseCODE
HIGHbackend/cli/src/compute/ssh/adapter.ts347 return FalseCODE
HIGHbackend/cli/src/compute/ssh/adapter.ts348 return TrueCODE
HIGHbackend/cli/src/compute/ssh/adapter.ts693 return NoneCODE
HIGHbackend/cli/src/compute/ssh/adapter.ts698 return FalseCODE
HIGHbackend/cli/src/compute/ssh/adapter.ts708 return FalseCODE
HIGHbackend/cli/src/compute/ssh/adapter.ts711 return FalseCODE
HIGHbackend/cli/src/compute/ssh/adapter.ts748 return TrueCODE
HIGHbackend/cli/src/compute/ssh/adapter.ts750 return FalseCODE
HIGHbackend/cli/src/compute/ssh/adapter.ts752 return FalseCODE
HIGHbackend/cli/src/compute/ssh/adapter.ts759 return FalseCODE
HIGHbackend/cli/src/compute/ssh/adapter.ts767 return TrueCODE
HIGHbackend/cli/src/compute/ssh/adapter.ts905 elif value["scheduler"] == "pbs":CODE
HIGHbackend/cli/src/compute/ssh/adapter.ts1151elif action == "submit": submit(token)CODE
HIGHbackend/cli/src/compute/ssh/adapter.ts1152elif action == "status": status(token, sys.argv[3])CODE
HIGHbackend/cli/src/compute/ssh/adapter.ts1153elif action == "cancel": cancel(token, sys.argv[3])CODE
HIGHbackend/cli/src/compute/ssh/adapter.ts1154elif action == "log": logs(token, sys.argv[3])CODE
HIGHbackend/cli/src/compute/ssh/adapter.ts1155elif action == "harvest": harvest(token)CODE
HIGHbackend/cli/src/compute/ssh/adapter.ts1156elif action == "release": release(token)CODE
HIGHbackend/cli/src/compute/ssh/adapter.ts214 return NoneCODE
HIGHbackend/cli/src/compute/ssh/adapter.ts245 return NoneCODE
HIGHbackend/cli/src/compute/ssh/adapter.ts460 return FalseCODE
HIGHbackend/cli/src/compute/ssh/adapter.ts462 return TrueCODE
HIGHbackend/cli/src/compute/ssh/adapter.ts1021 elif identifier.startswith("pbs:"):CODE
HIGHbackend/cli/src/compute/ssh/adapter.ts1041 elif not scope_empty(value):CODE
HIGHbackend/cli/src/compute/ssh/adapter.ts1218 print(json.dumps({"staged": True, "files": len(manifest["files"])}))CODE
HIGHbackend/cli/src/tool/biology/notebook.ts77 print(repr(result))CODE
Unused Imports181 hits · 160 pts
SeverityFileLineSnippetContext
LOW…esearch/perplexity-search/scripts/perplexity_search.py23CODE
LOW…esearch/perplexity-search/scripts/perplexity_search.py29CODE
LOW…alization/protein-diagram/scripts/draw_ramachandran.py28CODE
LOW…tion/dna-visualization/scripts/draw_restriction_map.py28CODE
LOW…tion/dna-visualization/scripts/draw_restriction_map.py29CODE
LOW…tion/dna-visualization/scripts/draw_restriction_map.py19CODE
LOW…visualization/matplotlib/scripts/style_configurator.py20CODE
LOW…ills/visualization/matplotlib/scripts/plot_template.py286CODE
LOW…tion/scientific-visualization/scripts/figure_export.py11CODE
LOW…tion/scientific-visualization/scripts/style_presets.py11CODE
LOW…ugging-face-tool-builder/references/baseline_hf_api.py9CODE
LOW…ills/databases/uspto-database/scripts/patent_search.py20CODE
LOW…ills/databases/uspto-database/scripts/patent_search.py21CODE
LOW…i/skills/databases/gene-database/scripts/query_gene.py16CODE
LOW…s/databases/biorxiv-database/scripts/biorxiv_search.py14CODE
LOW…s/databases/biorxiv-database/scripts/biorxiv_search.py17CODE
LOW…/databases/fred-economic-data/scripts/fred_examples.py9CODE
LOW…lls/databases/fred-economic-data/scripts/fred_query.py11CODE
LOW…databases/drugbank-database/scripts/drugbank_helper.py20CODE
LOW…abases/brenda-database/scripts/brenda_visualization.py26CODE
LOW…abases/brenda-database/scripts/brenda_visualization.py28CODE
LOW…abases/brenda-database/scripts/brenda_visualization.py28CODE
LOW…abases/brenda-database/scripts/brenda_visualization.py41CODE
LOW…abases/brenda-database/scripts/brenda_visualization.py41CODE
LOW…abases/brenda-database/scripts/brenda_visualization.py41CODE
LOW…abases/brenda-database/scripts/brenda_visualization.py41CODE
LOW…abases/brenda-database/scripts/brenda_visualization.py41CODE
LOW…ases/brenda-database/scripts/enzyme_pathway_builder.py27CODE
LOW…ases/brenda-database/scripts/enzyme_pathway_builder.py29CODE
LOW…ases/brenda-database/scripts/enzyme_pathway_builder.py29CODE
LOW…ases/brenda-database/scripts/enzyme_pathway_builder.py29CODE
LOW…ases/brenda-database/scripts/enzyme_pathway_builder.py30CODE
LOW…ases/brenda-database/scripts/enzyme_pathway_builder.py40CODE
LOW…ases/brenda-database/scripts/enzyme_pathway_builder.py54CODE
LOW…cli/skills/databases/fda-database/scripts/fda_query.py21CODE
LOW…cli/skills/databases/fda-database/scripts/fda_query.py22CODE
LOW…skills/databases/string-database/scripts/string_api.py17CODE
LOW…skills/databases/string-database/scripts/string_api.py18CODE
LOW…skills/databases/string-database/scripts/string_api.py18CODE
LOW…s/databases/uniprot-database/scripts/uniprot_client.py29CODE
LOW…/databases/reactome-database/scripts/reactome_query.py25CODE
LOW…linicaltrials-database/scripts/query_clinicaltrials.py16CODE
LOW…i/skills/chemistry/medchem/scripts/filter_molecules.py17CODE
LOW…i/skills/chemistry/medchem/scripts/filter_molecules.py18CODE
LOW…/chemistry/molecular-docking/scripts/prepare_target.py52CODE
LOW…chemistry/molecular-docking/scripts/prepare_ligands.py29CODE
LOW…chemistry/molecular-docking/scripts/prepare_ligands.py37CODE
LOW…cli/skills/chemistry/molecular-docking/scripts/dock.py22CODE
LOW…cli/skills/chemistry/molecular-docking/scripts/dock.py53CODE
LOW…li/skills/chemistry/molecular-docking/scripts/score.py17CODE
LOW…li/skills/chemistry/molecular-docking/scripts/score.py31CODE
LOW…li/skills/chemistry/molecular-docking/scripts/score.py31CODE
LOW…li/skills/chemistry/molecular-docking/scripts/score.py31CODE
LOW…li/skills/chemistry/molecular-docking/scripts/score.py32CODE
LOW…li/skills/chemistry/molecular-docking/scripts/score.py52CODE
LOW…li/skills/chemistry/molecular-docking/scripts/score.py52CODE
LOW…li/skills/chemistry/molecular-docking/scripts/score.py53CODE
LOW…lls/chemistry/structure-prediction/scripts/evaluate.py31CODE
LOW…ills/chemistry/structure-prediction/scripts/compare.py14CODE
LOW…ills/chemistry/structure-prediction/scripts/compare.py19CODE
121 more matches not shown…
Docstring Block Structure29 hits · 145 pts
SeverityFileLineSnippetContext
HIGH…cli/skills/databases/kegg-database/scripts/kegg_api.py44 List entry identifiers and associated names. Args: database: KEGG database name or specific entry (e.gSTRING
HIGH…cli/skills/databases/kegg-database/scripts/kegg_api.py72 Search for entries by keywords or molecular properties. Args: database: Database to search ('genes', 'STRING
HIGH…cli/skills/databases/kegg-database/scripts/kegg_api.py111 Retrieve full database entries or specific data formats. Args: entries: Single entry ID or list of entSTRING
HIGH…cli/skills/databases/kegg-database/scripts/kegg_api.py158 Convert identifiers between KEGG and external databases. Args: target_db: Target database (e.g., 'ncbiSTRING
HIGH…cli/skills/databases/kegg-database/scripts/kegg_api.py187 Find related entries across KEGG databases. Args: target_db: Target database (e.g., 'pathway', 'enzymeSTRING
HIGH…ls/databases/ensembl-database/scripts/ensembl_query.py58 Make an API request with error handling and retries. Args: endpoint: API endpoint path STRING
HIGH…skills/databases/string-database/scripts/string_api.py29 Map protein names, synonyms, and identifiers to STRING IDs. Args: identifiers: Single protein identifiSTRING
HIGH…skills/databases/string-database/scripts/string_api.py78 Get protein-protein interaction network data. Args: identifiers: Protein identifier(s) - use STRING IDSTRING
HIGH…ases/opentargets-database/scripts/query_opentargets.py22 Execute a GraphQL query against the Open Targets Platform API. Args: query: GraphQL query string STRING
HIGH…gineering/hugging-face-datasets/scripts/sql_manager.py134 Execute SQL query on a Hugging Face dataset. Args: dataset_id: Dataset ID (e.g., "cais/mmlSTRING
HIGH…gineering/hugging-face-datasets/scripts/sql_manager.py356 Filter and transform dataset with SQL clauses. Args: dataset_id: Dataset ID seSTRING
HIGH…d/cli/skills/ml-training/adaptyv/reference/examples.md505 Request a custom antigen not in the standard catalog Args: target_name: Name of the target protein STRING
HIGH…d/cli/skills/ml-training/adaptyv/reference/examples.md758 Make API request with retry logic and error handling Args: method: HTTP method (GET, POST, etc.) STRING
HIGH…kills/biology/clinical-imaging/scripts/hemodynamics.py37 Load blood pressure waveform data from CSV. Accepts CSV with columns 'time' and 'pressure', or just 'pressure'STRING
HIGH…kills/biology/clinical-imaging/scripts/ciliary_beat.py39 Load video frames as grayscale numpy array. Args: video_path: Path to video file. fps_overrideSTRING
HIGH…skills/biology/clinical-imaging/scripts/compute_adc.py46 Load diffusion-weighted NIfTI image. Args: dwi_path: Path to 4D NIfTI DWI file. Returns: STRING
HIGH…skills/biology/clinical-imaging/scripts/compute_adc.py75 Load binary brain mask NIfTI image. Args: mask_path: Path to 3D NIfTI mask file. Returns: STRING
HIGH…skills/biology/clinical-imaging/scripts/compute_adc.py104 Parse comma-separated b-value string into sorted numpy array. Args: bvalues_str: Comma-separated b-valSTRING
HIGH…ls/biology/clinical-imaging/scripts/amyloid_plaques.py46 Load microscopy image from file. Args: image_path: Path to image file (TIFF, PNG, JPEG, etc.). ReSTRING
HIGH…ls/biology/clinical-imaging/scripts/amyloid_plaques.py105 Threshold grayscale image to produce binary mask. Args: gray: 2D uint8 grayscale image (already smoothSTRING
HIGH…s/biology/clinical-imaging/scripts/cosinor_analysis.py41 Load time-series data from CSV. Expected columns: 'time' (hours) and 'value' (measurement). Args: STRING
HIGH…s/biology/clinical-imaging/scripts/cosinor_analysis.py99 Fit cosinor model to data using least-squares optimization. Args: time: 1D array of time points (hoursSTRING
HIGH…ls/biology/bioimage-analysis/scripts/colocalization.py38Load a single fluorescence channel image as a 2D grayscale array. Args: image_path: Path to the channel imaSTRING
HIGH…ls/biology/bioimage-analysis/scripts/colocalization.py82Apply a thresholding method to create a binary mask of signal pixels. Args: image: 2D float array of channeSTRING
HIGH…ls/biology/bioimage-analysis/scripts/count_colonies.py39Load an image from disk using OpenCV. Args: image_path: Path to the image file. Returns: numpySTRING
HIGH…iology/bioimage-analysis/scripts/analyze_morphology.py39Load a microscopy image from file. Args: image_path: Path to the image file. Returns: numpy.ndSTRING
HIGH…iology/bioimage-analysis/scripts/analyze_morphology.py75Load a pre-segmented integer label mask. Args: mask_path: Path to the mask image file. Returns: STRING
HIGH…kills/biology/bioimage-analysis/scripts/track_cells.py39Load time-lapse frames from a directory of images or a multi-frame TIFF. Args: image_source: Path to a direSTRING
HIGH…lls/biology/bioimage-analysis/scripts/segment_cells.py38Load a microscopy image from file. Supports TIFF (via tifffile), PNG, JPEG, and other formats via skimage. ArgSTRING
Verbosity Indicators73 hits · 125 pts
SeverityFileLineSnippetContext
LOWbackend/cli/test/agent/harness-contract.test.ts210 expect(skill).not.toContain("### Step 5: Save Report")CODE
LOW…s/databases/cosmic-database/scripts/download_cosmic.py64 # Step 1: Get the download URLCOMMENT
LOW…s/databases/cosmic-database/scripts/download_cosmic.py91 # Step 2: Download the fileCOMMENT
LOW…s/databases/cosmic-database/scripts/download_cosmic.py99 # Step 3: Write to diskCOMMENT
LOW…atabases/pubchem-database/scripts/bioactivity_query.py307 # Step 1: Find assays for the targetCOMMENT
LOW…atabases/pubchem-database/scripts/bioactivity_query.py314 # Step 2: Get active compounds from these assaysCOMMENT
LOW…s/databases/uniprot-database/scripts/uniprot_client.py164 # Step 1: Submit jobCOMMENT
LOW…s/databases/uniprot-database/scripts/uniprot_client.py177 # Step 2: Poll for completionCOMMENT
LOW…s/databases/uniprot-database/scripts/uniprot_client.py190 # Step 3: Retrieve resultsCOMMENT
LOW…s/databases/openalex-database/scripts/query_helpers.py28 # Step 1: Find author IDCOMMENT
LOW…s/databases/openalex-database/scripts/query_helpers.py43 # Step 2: Get works by authorCOMMENT
LOW…s/databases/openalex-database/scripts/query_helpers.py74 # Step 1: Find institution IDCOMMENT
LOW…s/databases/openalex-database/scripts/query_helpers.py89 # Step 2: Get works from institutionCOMMENT
LOW…s/databases/openalex-database/scripts/query_helpers.py234 # Step 1: Find entityCOMMENT
LOW…s/databases/openalex-database/scripts/query_helpers.py246 # Step 2: Get statisticsCOMMENT
LOW…skills/coding/pymoo/scripts/decision_making_example.py138 # Step 1: Run optimizationCOMMENT
LOW…skills/coding/pymoo/scripts/decision_making_example.py141 # Step 2: Find extreme solutionsCOMMENT
LOW…skills/coding/pymoo/scripts/decision_making_example.py144 # Step 3: Compare different preference weightsCOMMENT
LOW…skills/coding/pymoo/scripts/decision_making_example.py147 # Step 4: Visualize selections with petal diagramCOMMENT
LOW…/hugging-face-model-trainer/scripts/convert_to_gguf.py158# Step 2: Save merged model temporarilyCOMMENT
LOW…/hugging-face-model-trainer/scripts/convert_to_gguf.py169# Step 3: Install llama.cpp for conversionCOMMENT
LOW…/hugging-face-model-trainer/scripts/convert_to_gguf.py281# Step 6: Upload to HubCOMMENT
LOW…/hugging-face-model-trainer/scripts/convert_to_gguf.py121# Step 1: Load base model and adapterCOMMENT
LOW…/hugging-face-model-trainer/scripts/convert_to_gguf.py199# Step 4: Convert to GGUF (FP16)COMMENT
LOW…/hugging-face-model-trainer/scripts/convert_to_gguf.py223# Step 5: Quantize to different formatsCOMMENT
LOW…ls/biology/synthetic-biology/scripts/codon_optimize.py447 # Step 1: Replace with optimal codonsCOMMENT
LOW…ls/biology/synthetic-biology/scripts/codon_optimize.py457 # Step 2: Remove restriction sitesCOMMENT
LOW…ls/biology/synthetic-biology/scripts/codon_optimize.py460 # Step 3: Fix GC contentCOMMENT
LOW…ls/biology/synthetic-biology/scripts/codon_optimize.py463 # Step 4: Remove homopolymer runsCOMMENT
LOW…skills/biology/deeptools/scripts/workflow_generator.py72# Step 2: Coverage assessmentCOMMENT
LOW…skills/biology/deeptools/scripts/workflow_generator.py80# Step 3: Fragment size (for paired-end data)COMMENT
LOW…skills/biology/deeptools/scripts/workflow_generator.py87# Step 4: ChIP signal strengthCOMMENT
LOW…skills/biology/deeptools/scripts/workflow_generator.py307# Step 2: Generate coverage trackCOMMENT
LOW…skills/biology/deeptools/scripts/workflow_generator.py317# Step 3: Fragment size analysisCOMMENT
LOW…skills/biology/deeptools/scripts/workflow_generator.py324# Step 4: Compute matrix at peaks (if peaks provided)COMMENT
LOW…skills/biology/deeptools/scripts/workflow_generator.py51# Step 1: Correlation analysisCOMMENT
LOW…skills/biology/deeptools/scripts/workflow_generator.py128# Step 1: Generate normalized coverage tracksCOMMENT
LOW…skills/biology/deeptools/scripts/workflow_generator.py151# Step 2: Create log2 ratio trackCOMMENT
LOW…skills/biology/deeptools/scripts/workflow_generator.py164# Step 3: Compute matrix around TSSCOMMENT
LOW…skills/biology/deeptools/scripts/workflow_generator.py178# Step 4: Generate heatmapCOMMENT
LOW…skills/biology/deeptools/scripts/workflow_generator.py191# Step 5: Generate profile plotCOMMENT
LOW…skills/biology/deeptools/scripts/workflow_generator.py203# Step 6: Enrichment at peaks (if peaks provided)COMMENT
LOW…skills/biology/deeptools/scripts/workflow_generator.py294# Step 1: Shift reads for Tn5 correctionCOMMENT
LOW…gy/opentrons-integration/scripts/pcr_setup_template.py80 # Step 1: Distribute master mixCOMMENT
LOW…gy/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
LOW…iology/bioservices/scripts/compound_cross_reference.py337 # Step 1: Search KEGGSTRING
LOW…iology/bioservices/scripts/compound_cross_reference.py343 # Step 2: Get KEGG detailsSTRING
LOW…iology/bioservices/scripts/compound_cross_reference.py346 # Step 3: Map to ChEMBLSTRING
LOW…iology/bioservices/scripts/compound_cross_reference.py349 # Step 4: Get ChEBI detailsSTRING
LOW…iology/bioservices/scripts/compound_cross_reference.py354 # Step 5: Get ChEMBL detailsSTRING
LOW…ology/bioservices/scripts/protein_analysis_workflow.py368 # Step 1: Search proteinSTRING
LOW…ology/bioservices/scripts/protein_analysis_workflow.py374 # Step 2: Retrieve sequenceSTRING
LOW…ology/bioservices/scripts/protein_analysis_workflow.py379 # Step 3: BLAST searchSTRING
LOW…ology/bioservices/scripts/protein_analysis_workflow.py383 # Step 4: Pathway discoverySTRING
LOW…ology/bioservices/scripts/protein_analysis_workflow.py387 # Step 5: Interaction mappingSTRING
LOW…ology/bioservices/scripts/protein_analysis_workflow.py390 # Step 6: GO annotationsSTRING
LOW…skills/biology/gget/scripts/batch_sequence_analysis.py67 # Step 1: BLAST each sequenceCOMMENT
13 more matches not shown…
Hallucination Indicators11 hits · 125 pts
SeverityFileLineSnippetContext
CRITICALevals/launch/capture.ts501 `observable=${result.result.completion.observableComplete ? "complete" : "incomplete"} · ${result.result.observablCODE
CRITICALevals/cadence-harness/run.ts287 jobs = await unwrap<Json[]>(input.client.settings.compute.jobs.list())CODE
CRITICALfrontend/landing/public/docs/assets/index-Cazmh0hf.js731`,h="/",b="*",y="",S="comment",x="declaration";function T(Z,D){if(typeof Z!="string")throw new TypeError("First argumentCODE
CRITICALfrontend/landing/public/docs/assets/index-Cazmh0hf.js758`))}function m(x,T,U,Z){const D=U.enter("tableCell"),F=U.enter("phrasing"),Q=U.containerPhrasing(x,{...Z,before:d,after:CODE
CRITICAL…e/src/science/renderers/molecular/ProteinStructure.tsx94 subscriptions.push(p.managers.structure.selection.events.changed.subscribe(syncSelection))CODE
CRITICAL…e/src/science/renderers/molecular/ProteinStructure.tsx95 subscriptions.push(p.managers.structure.selection.events.additionsHistoryUpdated.subscribe(syncSelection))CODE
CRITICAL…e/src/science/renderers/molecular/ProteinStructure.tsx96 subscriptions.push(p.managers.structure.measurement.behaviors.state.subscribe(syncMeasurements))CODE
CRITICAL…ckend/cli/skills/ml-training/axolotl/references/api.md658core.trainers.grpo.sampler.SequenceParallelRepeatRandomSampler.set_epoch(epoch)CODE
CRITICAL…ckend/cli/skills/ml-training/axolotl/references/api.md1795core.trainers.grpo.trainer.AxolotlGRPOSequenceParallelTrainer.get_train_dataloader(CODE
CRITICAL…ckend/cli/skills/ml-training/axolotl/references/api.md4690core.trainers.dpo.trainer.AxolotlDPOTrainer.push_to_hub(*args, **kwargs)CODE
CRITICAL…ckend/cli/skills/ml-training/axolotl/references/api.md4892core.trainers.mixins.scheduler.SchedulerMixin.create_scheduler(CODE
Over-Commented Block130 hits · 124 pts
SeverityFileLineSnippetContext
LOWfrontend/ui/src/context/marked.tsx41 // "gitDecoration.untrackedResourceForeground": "#00cab1",COMMENT
LOWfrontend/ui/src/pierre/index.ts161 // numCol.dataset["slot"] = "diff-hunk-separator-line-number"COMMENT
LOWfrontend/workspace/src/components/terminal-error.ts1// When a pty socket dies, WebKit dispatches a bare `error` Event (no detail)COMMENT
LOWfrontend/workspace/src/components/settings/registry.ts1import { lazy, type Component } from "solid-js"COMMENT
LOWfrontend/workspace/src/atlas/poll-identity.ts1// A polling surface has to name itself to the server. Both compute samplersCOMMENT
LOWfrontend/workspace/src/atlas/FileExplorer.test.ts1import { describe, expect, test } from "bun:test"COMMENT
LOWbackend/cli/bunfig.toml1[test]COMMENT
LOWbackend/cli/parsers-config.ts141 // NOTE: This nvim-treesitter query is currently broken, because the parser is not compatible with the query aCOMMENT
LOWbackend/cli/test/preload.ts61COMMENT
LOWbackend/cli/test/auth/billing-flip.test.ts1import { test, expect, afterEach } from "bun:test"COMMENT
LOWbackend/cli/test/science/kernel/metrics.test.ts461COMMENT
LOWbackend/cli/test/science/kernel/metrics.test.ts801 // The grandchild alone holds 64MB the leader never touches, so theCOMMENT
LOWbackend/cli/test/provider/managed-routing.test.ts721 // google-vertex autoloads off GOOGLE_CLOUD_PROJECT alone (no auth.jsonCOMMENT
LOWbackend/cli/test/tool/question.test.ts61 askSpy.mockResolvedValueOnce([["Dog"]])COMMENT
LOWbackend/cli/test/tool/question.test.ts81 // } catch (e: any) {COMMENT
LOWbackend/cli/test/tool/question.test.ts101 // expect(true).toBe(false)COMMENT
LOW…conducting-scientific-research/references/templates.md1# Project record templatesCOMMENT
LOW…d/cli/skills/llm-tools/outlines/references/backends.md221# - Speed: Slightly slower than Q4COMMENT
LOW…databases/drugbank-database/references/drug-queries.md181# Common properties to extract:COMMENT
LOW…chemistry/diffdock/assets/custom_inference_config.yaml41COMMENT
LOW…chemistry/diffdock/assets/custom_inference_config.yaml61# temp_sampling_tor: 6.5COMMENT
LOW…chemistry/diffdock/assets/custom_inference_config.yaml81# temp_sampling_rot: 2.0COMMENT
LOW…skills/ml-inference/vllm/references/troubleshooting.md441COMMENT
LOW…skills/ml-inference/tensorrt-llm/references/serving.md161curl http://localhost:9090/metricsCOMMENT
LOW…/other/hugging-face-jobs/scripts/generate-responses.py1# /// scriptCOMMENT
LOW…s/other/hugging-face-jobs/scripts/cot-self-instruct.py1# /// scriptCOMMENT
LOW…cloud-compute/lambda-labs/references/advanced-usage.md281### Slurm job submissionCOMMENT
LOWbackend/cli/skills/data-engineering/markitdown/SKILL.md181COMMENT
LOW…d/cli/skills/coding/exploratory-data-analysis/SKILL.md301COMMENT
LOW…ckend/cli/skills/coding/denario/references/examples.md41### Execute Full PipelineCOMMENT
LOW…ckend/cli/skills/coding/denario/references/examples.md61# - Computed trend: +0.18°C per decadeCOMMENT
LOW…ckend/cli/skills/coding/denario/references/examples.md81# climate_research/COMMENT
LOW…ckend/cli/skills/coding/denario/references/examples.md421# - ROC curvesCOMMENT
LOW…ysics/pymatgen/references/transformations_workflows.md301 relax = MPRelaxSet(slab)COMMENT
LOWbackend/cli/skills/ml-training/moe-training/SKILL.md401COMMENT
LOW…training/accelerate/references/megatron-integration.md421# checkpoint-1000/COMMENT
LOW…cli/skills/ml-training/knowledge-distillation/SKILL.md221COMMENT
LOWbackend/cli/skills/ml-training/rwkv/SKILL.md141COMMENT
LOWbackend/cli/skills/ml-training/model-pruning/SKILL.md241- 50% sparsity (2:4) → 2× speedup on NVIDIA GPUsCOMMENT
LOW…g/prime-intellect-lab/templates/basic_rl_training.toml1# Prime Intellect Lab — RL Training ConfigurationCOMMENT
LOW…g/prime-intellect-lab/templates/basic_rl_training.toml21# "Qwen/Qwen3-235B-Instruct-2507" — Frontier-level (MoE)COMMENT
LOW…g/prime-intellect-lab/templates/basic_rl_training.toml41# LARGE RUN — Full training (~8-24 hours)COMMENT
LOW…g/prime-intellect-lab/templates/basic_rl_training.toml61id = "primeintellect/alphabet-sort" # Environment ID (owner/name)COMMENT
LOW…/skills/ml-training/gptq/references/troubleshooting.md61# Requantize with better calibrationCOMMENT
LOW…l-training/stable-baselines3/scripts/evaluate_agent.py201 # Example 1: Evaluate a trained modelCOMMENT
LOW…l-training/stable-baselines3/scripts/evaluate_agent.py221 # watch_agent(COMMENT
LOW…l-training/stable-baselines3/scripts/evaluate_agent.py241 # model_path="./models/best_model/best_model.zip",COMMENT
LOW…l-training/stable-baselines3/scripts/train_rl_agent.py141 algorithm=PPO,COMMENT
LOW…l-training/stable-baselines3/scripts/train_rl_agent.py161 # algorithm=DQN,COMMENT
LOW…ining/stable-baselines3/scripts/custom_env_template.py61 # 2. Multi-discrete: spaces.MultiDiscrete([n1, n2, ...])COMMENT
LOW…gging-face-model-trainer/references/gguf_conversion.md61### 3. ✅ Include All DependenciesCOMMENT
LOW…ace-model-trainer/references/reliability_principles.md161# ///COMMENT
LOW…/hugging-face-model-trainer/scripts/convert_to_gguf.py1#!/usr/bin/env python3COMMENT
LOW…ugging-face-model-trainer/scripts/train_sft_example.py1#!/usr/bin/env python3COMMENT
LOW…end/cli/skills/ml-training/axolotl/references/other.md1841 # The name of the chat template to use for training, following values are supported:COMMENT
LOW…end/cli/skills/ml-training/axolotl/references/other.md1881 # message_property_mappings={'role':'role', 'content':'content'}) If a property existsCOMMENT
LOW…end/cli/skills/ml-training/axolotl/references/other.md1901 # Roles to train on. The tokens from these roles will be considered for the loss.COMMENT
LOW…end/cli/skills/ml-training/axolotl/references/other.md2001 # will raise an error. This is the default.COMMENT
LOW…end/cli/skills/ml-training/axolotl/references/other.md2041 # 'from' is loaded from input dataset and used as 'role', while 'value' is loaded andCOMMENT
LOW…end/cli/skills/ml-training/axolotl/references/other.md2061 # all EOS tokens, turn (default): train on the EOS token at the end of each trainableCOMMENT
70 more matches not shown…
Redundant / Tautological Comments79 hits · 104 pts
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LOW…esearch/perplexity-search/scripts/perplexity_search.py120 # Check if citations are available in the responseCOMMENT
LOW…cli/skills/research/research-lookup/research_lookup.py432 # Display results in human-readable formatCOMMENT
LOW…ls/research/research-lookup/scripts/research_lookup.py432 # Display results in human-readable formatCOMMENT
LOW…scientific-schematics/scripts/generate_schematic_ai.py712 # Check if quality is acceptable - STOP EARLY if soCOMMENT
LOW…zation/infographics/scripts/generate_infographic_ai.py1149 # Check if quality is acceptableSTRING
LOW…g-face-tool-builder/references/find_models_by_paper.sh93# Check if the input looks like an arXiv ID (format: YYYY.NNNNN or YYYY.NNNNNNN)COMMENT
LOW…g-face-tool-builder/references/find_models_by_paper.sh133# Check if we got a valid responseCOMMENT
LOW…ills/databases/uspto-database/scripts/patent_search.py281 # Print resultsCOMMENT
LOW…s/databases/gene-database/scripts/batch_gene_lookup.py281 # Output resultsSTRING
LOW…s/databases/biorxiv-database/scripts/biorxiv_search.py224 # Check if any keyword matchesCOMMENT
LOW…s/databases/biorxiv-database/scripts/biorxiv_search.py418 # Output resultsCOMMENT
LOW…ls/databases/brenda-database/scripts/brenda_queries.py220 # Check if our target product is in the products listCOMMENT
LOW…ls/databases/brenda-database/scripts/brenda_queries.py590 # Check if organism might be thermophilic based on nameCOMMENT
LOW…ases/brenda-database/scripts/enzyme_pathway_builder.py287 # Check if substrate is in the reactantsCOMMENT
LOW…ases/brenda-database/scripts/enzyme_pathway_builder.py302 # Check if product is mentioned in substrate data (limited approach)COMMENT
LOW…ases/brenda-database/scripts/enzyme_pathway_builder.py184 # Check if it's in the databaseCOMMENT
LOW…ases/brenda-database/scripts/enzyme_pathway_builder.py380 # Check if current metabolite is a starting materialCOMMENT
LOW…cli/skills/databases/fda-database/scripts/fda_query.py40 # Check if at limitCOMMENT
LOW…databases/openalex-database/scripts/openalex_client.py222 # Check if we've hit max_resultsCOMMENT
LOW…databases/openalex-database/scripts/openalex_client.py226 # Check if there are more pagesCOMMENT
LOW…linicaltrials-database/scripts/query_clinicaltrials.py158 # Check if we've reached the max or there are no more resultsCOMMENT
LOW…chemistry/molecular-docking/scripts/prepare_ligands.py162 # Check if input is a fileCOMMENT
LOW…cli/skills/chemistry/molecular-docking/scripts/dock.py61 # Check if DiffDock CLI is availableCOMMENT
LOW…ls/chemistry/admet-prediction/scripts/compare_drugs.py523 # Print resultsSTRING
LOW…i/skills/chemistry/diffdock/scripts/analyze_results.py36 # Check if this is a single complex or batch resultsCOMMENT
LOW…skills/chemistry/diffdock/scripts/prepare_batch_csv.py130 # Check if it's a file path or SMILESCOMMENT
LOW…skills/chemistry/binding-affinity/scripts/consensus.py132 # Check if it's rescore or interactionsCOMMENT
LOW…kills/chemistry/deepchem/scripts/predict_solubility.py150 # Display resultsCOMMENT
LOW…kills/chemistry/denovo-design/scripts/generate_sbdd.py205 # Check if this residue matches any specifiedCOMMENT
LOW…li/skills/chemistry/rdkit/scripts/similarity_search.py288 # Output resultsSTRING
LOW…skills/chemistry/rdkit/scripts/molecular_properties.py131 # Output resultsCOMMENT
LOW…li/skills/chemistry/pocket-detection/scripts/detect.py735 # Print resultsSTRING
LOW…er/get-available-resources/scripts/detect_resources.py155 # Check if running on Apple SiliconCOMMENT
LOW…/other/iso-13485-certification/scripts/gap_analyzer.py208 # Read file content (simple text reading)COMMENT
LOW…/other/iso-13485-certification/scripts/gap_analyzer.py231 # Check if any keyword appears in the documentCOMMENT
LOW…s/other/hugging-face-jobs/scripts/cot-self-instruct.py309 # Check if majority answer matches original and meets thresholdCOMMENT
LOW…ills/other/hugging-face-jobs/scripts/finepdfs-stats.py423 # Print resultsSTRING
LOW…s/other/labarchive-integration/scripts/setup_config.py167 # Check if config already existsCOMMENT
LOW…end/cli/skills/coding/pymc/scripts/model_comparison.py104 # Check if difference is significant relative to SECOMMENT
LOW…ding/statistical-analysis/scripts/assumption_checks.py453 # Check if grouped dataCOMMENT
LOW…ills/coding/torch_geometric/scripts/visualize_graph.py159 # Check if all edges have their reverseCOMMENT
LOW…/skills/coding/pymoo/scripts/many_objective_example.py44 # Print results summaryCOMMENT
LOW…kills/coding/pymoo/scripts/single_objective_example.py45 # Print resultsCOMMENT
LOW…skills/coding/pymoo/scripts/multi_objective_example.py36 # Print results summaryCOMMENT
LOW…/hugging-face-evaluation/scripts/evaluation_manager.py128 # Check if first column looks like benchmark namesCOMMENT
LOW…/hugging-face-evaluation/scripts/evaluation_manager.py138 # Check if there are numeric values in the tableCOMMENT
LOW…/hugging-face-evaluation/scripts/evaluation_manager.py281 # Check if first column header suggests model namesCOMMENT
LOW…/hugging-face-evaluation/scripts/evaluation_manager.py286 # Check if remaining headers look like benchmarksCOMMENT
LOW…/hugging-face-evaluation/scripts/evaluation_manager.py301 # Check if data rows have numeric values in most columns (except first)COMMENT
LOW…/hugging-face-evaluation/scripts/evaluation_manager.py346 # Check if first column header is empty/generic (indicates benchmarks in rows)COMMENT
LOW…ining/stable-baselines3/scripts/custom_env_template.py135 # Check if goal is reachedCOMMENT
LOW…i/skills/ml-training/pufferlib/scripts/env_template.py102 # Check if episode is doneCOMMENT
LOW…ills/biology/synthetic-biology/scripts/gene_circuit.py250 # Check if this is a new steady stateCOMMENT
LOW…kills/biology/clinical-imaging/scripts/ciliary_beat.py154 # Check if signal has variance (cilia must be beating)COMMENT
LOW…s/biology/clinical-imaging/scripts/cosinor_analysis.py313 # Print resultsSTRING
LOW…cli/skills/biology/deeptools/scripts/validate_files.py61 # Check if start and end are integersCOMMENT
LOW…cli/skills/biology/deeptools/scripts/validate_files.py168 # Check if any files were providedSTRING
LOW…cli/skills/biology/deeptools/scripts/validate_files.py180 # Print resultsSTRING
LOW…skills/biology/deeptools/scripts/workflow_generator.py417 # Check if workflow was specifiedSTRING
LOW…/biology/treatment-plans/scripts/check_completeness.py295 # Read fileSTRING
19 more matches not shown…
Cross-File Repetition13 hits · 65 pts
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HIGH…scientific-schematics/scripts/generate_schematic_ai.py0return only a user-owned openrouter key, never a managed proxy token.STRING
HIGH…lls/llm-tools/generate-image/scripts/generate_image.py0return only a user-owned openrouter key, never a managed proxy token.STRING
HIGH…g/scientific-slides/scripts/generate_slide_image_ai.py0return only a user-owned openrouter key, never a managed proxy token.STRING
HIGH…scientific-schematics/scripts/generate_schematic_ai.py0keep byok off the synthetic sciences credits proxy if a stale base url leaked in.STRING
HIGH…lls/llm-tools/generate-image/scripts/generate_image.py0keep byok off the synthetic sciences credits proxy if a stale base url leaked in.STRING
HIGH…g/scientific-slides/scripts/generate_slide_image_ai.py0keep byok off the synthetic sciences credits proxy if a stale base url leaked in.STRING
HIGH…ls/chemistry/admet-prediction/scripts/drug_likeness.py0parse input: smiles string or csv file. returns list of (name, mol).STRING
HIGH…chemistry/admet-prediction/scripts/predict_toxicity.py0parse input: smiles string or csv file. returns list of (name, mol).STRING
HIGH…ls/chemistry/admet-prediction/scripts/compare_drugs.py0parse input: smiles string or csv file. returns list of (name, mol).STRING
HIGH…iology/molecular-cloning/scripts/restriction_digest.py0return an uppercase dna string from a fasta file or raw sequence.STRING
HIGH…ills/biology/molecular-cloning/scripts/simulate_pcr.py0return an uppercase dna string from a fasta file or raw sequence.STRING
HIGH…lls/biology/molecular-cloning/scripts/design_crispr.py0return an uppercase dna string from a fasta file or raw sequence.STRING
HIGH…ls/biology/molecular-cloning/scripts/design_primers.py0return an uppercase dna string from a fasta file or raw sequence.STRING
AI Slop Vocabulary27 hits · 52 pts
SeverityFileLineSnippetContext
MEDIUMevals/cadence-harness/prepare.ts157 `# Better search and parallelism backlog\n\nUpdated after each three-run batch. Items stay here when the trajectorCODE
MEDIUMfrontend/landing/public/docs/assets/index-Cazmh0hf.js49`).replace(jb,"")}function ap(e,t){return t=ip(t),ip(e)===t}function Be(e,t,l,i,u,s){switch(l){case"children":typeof i==CODE
MEDIUMfrontend/landing/public/docs/assets/index-Cazmh0hf.js140`,C1='---\ntitle: "Command reference"\ndescription: "Every openscience subcommand: workspace, run, sessions, models, ageCODE
MEDIUMfrontend/landing/public/docs/assets/index-Cazmh0hf.js552`,D1='---\ntitle: "Sessions & one-shot runs"\ndescription: "One agent conversation: history, tool calls, and a working dCODE
MEDIUMfrontend/landing/public/docs/assets/index-Cazmh0hf.js730`,N1="https://mintlify.com/docs.json",L1="OpenScience",U1={tabs:[{tab:"Guides",groups:[{group:"Start",pages:["index","quCODE
MEDIUMfrontend/workspace/e2e/skills.spec.ts48// top). Kept fixme until the click is made robust against that quirk.COMMENT
MEDIUMbackend/cli/test/tool/question.test.ts73 // header: "This Header is Definitely More Than Thirty Characters Long",COMMENT
MEDIUM…cli/skills/research/research-lookup/research_lookup.py143 return f"""You are an expert research assistant. Please provide comprehensive, accurate research information forCODE
MEDIUM…ls/research/research-lookup/scripts/research_lookup.py143 return f"""You are an expert research assistant. Please provide comprehensive, accurate research information forCODE
MEDIUM…et-research-reports/scripts/generate_market_visuals.py15 # Generate all 28 visuals (for comprehensive coverage)STRING
MEDIUM…scientific-schematics/scripts/generate_schematic_ai.py115 # Scientific diagram best practices prompt templateCOMMENT
MEDIUM…ills/visualization/matplotlib/scripts/plot_template.py317 """Create a comprehensive figure with multiple subplots."""STRING
MEDIUM…abases/brenda-database/scripts/brenda_visualization.py682 """Generate a comprehensive set of plots for an enzyme."""STRING
MEDIUM…ases/brenda-database/scripts/enzyme_pathway_builder.py806 """Generate a comprehensive pathway report."""STRING
LOW…cli/skills/chemistry/molecular-docking/scripts/rank.py423 "composite_score": entry["score"], # just use raw scoreCODE
MEDIUM…chemistry/admet-prediction/scripts/predict_toxicity.py69# AMES mutagenicity: comprehensive structural alert library (~30 patterns)COMMENT
MEDIUM…skills/chemistry/rdkit/scripts/molecular_properties.py26 """Calculate comprehensive molecular properties."""STRING
MEDIUM…/other/iso-13485-certification/scripts/gap_analyzer.py250 """Generate comprehensive gap analysis report."""STRING
MEDIUM…/other/hugging-face-jobs/scripts/generate-responses.py94 """Create a comprehensive dataset card documenting the generation process."""STRING
MEDIUM…s/other/hugging-face-jobs/scripts/cot-self-instruct.py374 """Create a comprehensive dataset card."""STRING
MEDIUM…/skills/scholar-evaluation/scripts/calculate_scores.py148 """Generate comprehensive evaluation report."""STRING
MEDIUM…ding/statistical-analysis/scripts/assumption_checks.py186 # Levene's test (robust to non-normality)COMMENT
MEDIUM…ding/statistical-analysis/scripts/assumption_checks.py533 # Run comprehensive checkCOMMENT
MEDIUM…ogy/treatment-plans/scripts/validate_treatment_plan.py179 """Display comprehensive validation results."""STRING
MEDIUM…/biology/flow-cytometry-analysis/scripts/cell_cycle.py122 # Filter out extreme outliers for robust peak detectionCOMMENT
MEDIUM…ology/clinical-reports/scripts/validate_case_report.py192 """Generate comprehensive validation report."""STRING
MEDIUM…ls/biology/pharmacology-wetlab/scripts/western_blot.py84 # Simple equal-width fallback (robust for most gel images)COMMENT
Example Usage Blocks24 hits · 38 pts
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LOW…tion/scientific-visualization/scripts/figure_export.py318 # Example usageCOMMENT
LOW…cli/skills/databases/kegg-database/scripts/kegg_api.py242 # Example usageCOMMENT
LOW…databases/drugbank-database/scripts/drugbank_helper.py307# Example usageCOMMENT
LOW…abases/brenda-database/scripts/brenda_visualization.py744 # Example usageCOMMENT
LOW…ls/databases/brenda-database/scripts/brenda_queries.py814 # Example usageCOMMENT
LOW…ases/brenda-database/scripts/enzyme_pathway_builder.py1014 # Example usageCOMMENT
LOW…skills/databases/string-database/scripts/string_api.py357 # Example usageCOMMENT
LOW…s/databases/openalex-database/scripts/query_helpers.py293 # Example usageCOMMENT
LOW…databases/openalex-database/scripts/openalex_client.py325 # Example usageCOMMENT
LOW…s/databases/chembl-database/scripts/example_queries.py254# Example usageCOMMENT
LOW…linicaltrials-database/scripts/query_clinicaltrials.py196# Example usageCOMMENT
LOW…ases/opentargets-database/scripts/query_opentargets.py369# Example usageSTRING
LOW…end/cli/skills/coding/pymc/scripts/model_comparison.py358# Example usageSTRING
LOW…nd/cli/skills/coding/pymc/scripts/model_diagnostics.py328# Example usageCOMMENT
LOW…ding/statistical-analysis/scripts/assumption_checks.py521 # Example usageCOMMENT
LOW…nd/cli/skills/coding/simpy/scripts/resource_monitor.py320# Example usageCOMMENT
LOW…lls/coding/scikit-learn/scripts/clustering_analysis.py338# Example usageCOMMENT
LOW…coding/scikit-learn/scripts/classification_pipeline.py230# Example usageCOMMENT
LOW…g/prime-intellect-lab/templates/basic_rl_training.toml4# Usage:COMMENT
LOW…decision-support/scripts/generate_survival_analysis.py433# Example usage:COMMENT
LOW…ical-decision-support/scripts/validate_cds_document.py323# Example usage:COMMENT
LOW…nical-decision-support/scripts/biomarker_classifier.py375# Example usage:COMMENT
LOW…inical-decision-support/scripts/build_decision_tree.py412# Example usage:COMMENT
LOW…nical-decision-support/scripts/create_cohort_tables.py501# Example usage:COMMENT
Self-Referential Comments9 hits · 27 pts
SeverityFileLineSnippetContext
MEDIUMfrontend/landing/public/docs/assets/index-Cazmh0hf.js87## Create a custom agentCOMMENT
MEDIUM…ls/chemistry/molecule-visualization/scripts/draw_2d.py106 # Create the drawerCOMMENT
MEDIUM…ls/chemistry/hypogenic/references/config_template.yaml116# Define a custom function in your code to parse specific output formatsCOMMENT
MEDIUM…ering/hugging-face-datasets/scripts/dataset_manager.py53 # Create a basic README.md with metadata if it doesn't existCOMMENT
MEDIUM…ering/hugging-face-datasets/scripts/dataset_manager.py286 # Create a newline-delimited JSON stringCOMMENT
MEDIUM…ills/coding/torch_geometric/scripts/visualize_graph.py155 # Create a set of edges and reverse edgesCOMMENT
MEDIUM…/skills/coding/pymoo/scripts/many_objective_example.py19 # Define the problem - DTLZ2 with 5 objectivesCOMMENT
MEDIUM…kills/coding/pymoo/scripts/single_objective_example.py21 # Define the problem - Sphere function (sum of squares)COMMENT
MEDIUM…skills/coding/pymoo/scripts/multi_objective_example.py18 # Define the problem - ZDT1 (bi-objective)COMMENT
Cross-Language Confusion6 hits · 22 pts
SeverityFileLineSnippetContext
HIGH…ing/hugging-face-evaluation/scripts/test_extraction.py15Run from the scripts/ directory: cd scripts && uv run test_extraction.pySTRING
HIGH…/hugging-face-model-trainer/scripts/convert_to_gguf.py70 print(" macOS: xcode-select --install && brew install cmake")CODE
HIGH…/hugging-face-model-trainer/scripts/convert_to_gguf.py27- Ubuntu/Debian: sudo apt-get update && sudo apt-get install -y build-essential cmakeSTRING
HIGH…/hugging-face-model-trainer/scripts/convert_to_gguf.py29- macOS: xcode-select --install && brew install cmakeSTRING
HIGH…/biology/treatment-plans/scripts/check_completeness.py265 python check_completeness.py plan.tex && echo "Complete"CODE
HIGH…ogy/treatment-plans/scripts/validate_treatment_plan.py316 python validate_treatment_plan.py plan.tex && echo "Quality check passed"CODE
Fake / Example Data20 hits · 19 pts
SeverityFileLineSnippetContext
LOWfrontend/ui/src/components/line-comment.tsx102 "placeholder",CODE
LOWfrontend/ui/src/components/select.tsx28 "placeholder",CODE
LOW…nd/workspace/src/components/prompt-placeholder.test.ts25 expect(source).not.toContain('setStore("placeholder"')CODE
LOW…rkspace/src/components/settings/network-domain.test.ts16 "user@example.org",CODE
LOWbackend/cli/test/tool/research-contract.test.ts134 metric: { name: "placeholder", value: 0, direction: "maximize", baseline: 0, target: 0, unit: "none" },CODE
LOWbackend/cli/skills/llm-tools/dspy/SKILL.md355print(result.person.name) # "John Doe"CODE
LOWbackend/cli/skills/llm-tools/dspy/references/modules.md236print(result.person.name) # "John Doe"CODE
LOW…nd/cli/skills/llm-tools/langchain/references/agents.md137 ("placeholder", "{agent_scratchpad}"),CODE
LOWbackend/cli/skills/llm-tools/outlines/SKILL.md75print(user.name) # "John Doe"CODE
LOWbackend/cli/skills/llm-tools/instructor/SKILL.md67print(user.name) # "John Doe"CODE
LOWbackend/cli/skills/llm-tools/instructor/SKILL.md633 "name": "John Doe",STRING
LOWbackend/cli/skills/llm-tools/instructor/SKILL.md675 "name": "John Doe",CODE
LOW…s/databases/cosmic-database/scripts/download_cosmic.py13 email="user@example.com",STRING
LOW…/writing/pptx-posters/assets/poster_html_template.html206 <div id="chart1" class="placeholder" style="width: 100%; height: 400pt;"></div>CODE
LOW…riting/pptx-posters/assets/poster_quality_checklist.md15- [ ] No placeholder text remaining (TODO, Lorem ipsum, etc.)CODE
LOWbackend/cli/skills/writing/latex-posters/SKILL.md1075- [ ] No placeholder text remaining (Lorem ipsum, TODO, etc.)CODE
LOW…/skills/writing/latex-posters/scripts/review_poster.sh179echo " [ ] No placeholder text (Lorem ipsum, TODO, etc.)"CODE
LOW…iting/latex-posters/assets/poster_quality_checklist.md15- [ ] No placeholder text remaining (TODO, Lorem ipsum, etc.)CODE
LOWbackend/cli/skills/writing/ml-paper-writing/SKILL.md604% - Lorem ipsum or placeholder textCODE
LOWbackend/cli/src/auth/index.ts10export const OAUTH_DUMMY_KEY = "synsc-oauth-dummy-key"CODE
AI Structural Patterns14 hits · 13 pts
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LOW…lls/databases/fred-economic-data/scripts/fred_query.py113CODE
LOW…lls/databases/fred-economic-data/scripts/fred_query.py162CODE
LOW…linicaltrials-database/scripts/query_clinicaltrials.py22CODE
LOW…cli/skills/chemistry/molecular-docking/scripts/dock.py541CODE
LOW…cli/skills/chemistry/molecular-docking/scripts/dock.py811CODE
LOW…/other/hugging-face-jobs/scripts/generate-responses.py168CODE
LOW…ills/coding/torch_geometric/scripts/visualize_graph.py27CODE
LOW…ing/hugging-face-evaluation/scripts/inspect_vllm_uv.py49CODE
LOW…g/hugging-face-evaluation/scripts/lighteval_vllm_uv.py45CODE
LOW…l-training/stable-baselines3/scripts/train_rl_agent.py24CODE
LOW…ls/biology/molecular-cloning/scripts/design_primers.py87CODE
LOW…nical-decision-support/scripts/create_cohort_tables.py416CODE
LOW…y/neuropixels-analysis/scripts/preprocess_recording.py15CODE
LOW…s/biology/pharmacology-wetlab/scripts/dose_response.py215CODE
AI Response Leakage2 hits · 10 pts
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HIGHbackend/cli/skills/ml-training/deepspeed/SKILL.md65**Pattern 7:** DeepSpeed Configuration JSON Contents Batch Size Related Parameters Optimizer Parameters Scheduler ParameCODE
HIGHbackend/cli/skills/ml-training/pytorch-fsdp/SKILL.md35**Pattern 2:** Distributed communication package - torch.distributed# Created On: Jul 12, 2017 | Last Updated On: Sep 04CODE
Synthetic Comment Markers1 hit · 5 pts
SeverityFileLineSnippetContext
HIGHbackend/cli/skills/writing/latex-posters/SKILL.md113The #1 issue with AI-generated poster graphics is **TOO MUCH CONTENT**. This causes:CODE
Modern Structural Boilerplate4 hits · 4 pts
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LOW…tion/scientific-visualization/scripts/style_presets.py195def set_color_palette(palette_name: str = 'okabe_ito') -> None:CODE
LOW…/other/hugging-face-jobs/scripts/generate-responses.py61logger = logging.getLogger(__name__)CODE
LOW…s/other/hugging-face-jobs/scripts/cot-self-instruct.py75logger = logging.getLogger(__name__)CODE
LOW…ills/other/hugging-face-jobs/scripts/finepdfs-stats.py53logger = logging.getLogger(__name__)CODE
Slop Phrases1 hit · 2 pts
SeverityFileLineSnippetContext
MEDIUM…/hugging-face-datasets/examples/training_examples.json111 "content": "Great! I've fixed the missing config file issue. Your Node.js app should now start without crashing.CODE