Turn any AI agent into an AI Scientist. The #1 Agent Skills library for science, used by 160,000+ scientists worldwide. 140 ready-to-use skills plus 100+ scientific databases covering biology, chemistry, medicine, and drug discovery. Compatible with Cursor, Claude Code, Codex, Antigravity, and the open Agent Skills standard.
2098 matches across 16 categories. Click a row to expand file-level details.
| Severity | File | Line | Snippet |
|---|---|---|---|
| HIGH | skills/research-lookup/scripts/generate_schematic_ai.py | 0 | ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: |
| HIGH | …scientific-schematics/scripts/generate_schematic_ai.py | 0 | ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: |
| HIGH | …s/citation-management/scripts/generate_schematic_ai.py | 0 | ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: |
| HIGH | skills/markitdown/scripts/generate_schematic_ai.py | 0 | ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: |
| HIGH | skills/pptx-posters/scripts/generate_schematic_ai.py | 0 | ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: |
| HIGH | skills/treatment-plans/scripts/generate_schematic_ai.py | 0 | ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: |
| HIGH | …ls/scientific-writing/scripts/generate_schematic_ai.py | 0 | ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: |
| HIGH | …ical-decision-support/scripts/generate_schematic_ai.py | 0 | ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: |
| HIGH | …lls/literature-review/scripts/generate_schematic_ai.py | 0 | ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: |
| HIGH | …ls/scholar-evaluation/scripts/generate_schematic_ai.py | 0 | ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: |
| HIGH | skills/latex-posters/scripts/generate_schematic_ai.py | 0 | ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: |
| HIGH | skills/venue-templates/scripts/generate_schematic_ai.py | 0 | ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: |
| HIGH | …ills/clinical-reports/scripts/generate_schematic_ai.py | 0 | ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: |
| HIGH | …lls/scientific-slides/scripts/generate_schematic_ai.py | 0 | ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: |
| HIGH | …hypothesis-generation/scripts/generate_schematic_ai.py | 0 | ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: |
| HIGH | skills/peer-review/scripts/generate_schematic_ai.py | 0 | ai-powered scientific schematic generation using nano banana 2. this script uses a smart iterative refinement approach: |
| HIGH | skills/research-lookup/scripts/generate_schematic_ai.py | 0 | load .env file from current directory or script directory only. |
| HIGH | …scientific-schematics/scripts/generate_schematic_ai.py | 0 | load .env file from current directory or script directory only. |
| HIGH | …s/citation-management/scripts/generate_schematic_ai.py | 0 | load .env file from current directory or script directory only. |
| HIGH | skills/markitdown/scripts/generate_schematic_ai.py | 0 | load .env file from current directory or script directory only. |
| HIGH | skills/infographics/scripts/generate_infographic_ai.py | 0 | load .env file from current directory or script directory only. |
| HIGH | skills/pptx-posters/scripts/generate_schematic_ai.py | 0 | load .env file from current directory or script directory only. |
| HIGH | skills/treatment-plans/scripts/generate_schematic_ai.py | 0 | load .env file from current directory or script directory only. |
| HIGH | …ls/scientific-writing/scripts/generate_schematic_ai.py | 0 | load .env file from current directory or script directory only. |
| HIGH | …ical-decision-support/scripts/generate_schematic_ai.py | 0 | load .env file from current directory or script directory only. |
| HIGH | …lls/literature-review/scripts/generate_schematic_ai.py | 0 | load .env file from current directory or script directory only. |
| HIGH | …ls/scholar-evaluation/scripts/generate_schematic_ai.py | 0 | load .env file from current directory or script directory only. |
| HIGH | skills/latex-posters/scripts/generate_schematic_ai.py | 0 | load .env file from current directory or script directory only. |
| HIGH | skills/venue-templates/scripts/generate_schematic_ai.py | 0 | load .env file from current directory or script directory only. |
| HIGH | …ills/clinical-reports/scripts/generate_schematic_ai.py | 0 | load .env file from current directory or script directory only. |
| HIGH | …lls/scientific-slides/scripts/generate_schematic_ai.py | 0 | load .env file from current directory or script directory only. |
| HIGH | …s/scientific-slides/scripts/generate_slide_image_ai.py | 0 | load .env file from current directory or script directory only. |
| HIGH | …hypothesis-generation/scripts/generate_schematic_ai.py | 0 | load .env file from current directory or script directory only. |
| HIGH | skills/peer-review/scripts/generate_schematic_ai.py | 0 | load .env file from current directory or script directory only. |
| HIGH | skills/research-lookup/scripts/generate_schematic_ai.py | 0 | generate scientific schematics using ai with smart iterative refinement. uses gemini 3.1 pro preview for quality review |
| HIGH | …scientific-schematics/scripts/generate_schematic_ai.py | 0 | generate scientific schematics using ai with smart iterative refinement. uses gemini 3.1 pro preview for quality review |
| HIGH | …s/citation-management/scripts/generate_schematic_ai.py | 0 | generate scientific schematics using ai with smart iterative refinement. uses gemini 3.1 pro preview for quality review |
| HIGH | skills/markitdown/scripts/generate_schematic_ai.py | 0 | generate scientific schematics using ai with smart iterative refinement. uses gemini 3.1 pro preview for quality review |
| HIGH | skills/pptx-posters/scripts/generate_schematic_ai.py | 0 | generate scientific schematics using ai with smart iterative refinement. uses gemini 3.1 pro preview for quality review |
| HIGH | skills/treatment-plans/scripts/generate_schematic_ai.py | 0 | generate scientific schematics using ai with smart iterative refinement. uses gemini 3.1 pro preview for quality review |
| HIGH | …ls/scientific-writing/scripts/generate_schematic_ai.py | 0 | generate scientific schematics using ai with smart iterative refinement. uses gemini 3.1 pro preview for quality review |
| HIGH | …ical-decision-support/scripts/generate_schematic_ai.py | 0 | generate scientific schematics using ai with smart iterative refinement. uses gemini 3.1 pro preview for quality review |
| HIGH | …lls/literature-review/scripts/generate_schematic_ai.py | 0 | generate scientific schematics using ai with smart iterative refinement. uses gemini 3.1 pro preview for quality review |
| HIGH | …ls/scholar-evaluation/scripts/generate_schematic_ai.py | 0 | generate scientific schematics using ai with smart iterative refinement. uses gemini 3.1 pro preview for quality review |
| HIGH | skills/latex-posters/scripts/generate_schematic_ai.py | 0 | generate scientific schematics using ai with smart iterative refinement. uses gemini 3.1 pro preview for quality review |
| HIGH | skills/venue-templates/scripts/generate_schematic_ai.py | 0 | generate scientific schematics using ai with smart iterative refinement. uses gemini 3.1 pro preview for quality review |
| HIGH | …ills/clinical-reports/scripts/generate_schematic_ai.py | 0 | generate scientific schematics using ai with smart iterative refinement. uses gemini 3.1 pro preview for quality review |
| HIGH | …lls/scientific-slides/scripts/generate_schematic_ai.py | 0 | generate scientific schematics using ai with smart iterative refinement. uses gemini 3.1 pro preview for quality review |
| HIGH | …hypothesis-generation/scripts/generate_schematic_ai.py | 0 | generate scientific schematics using ai with smart iterative refinement. uses gemini 3.1 pro preview for quality review |
| HIGH | skills/peer-review/scripts/generate_schematic_ai.py | 0 | generate scientific schematics using ai with smart iterative refinement. uses gemini 3.1 pro preview for quality review |
| HIGH | skills/research-lookup/scripts/generate_schematic_ai.py | 0 | create a high-quality scientific diagram with these requirements: visual quality: - clean white or light background (no |
| HIGH | …scientific-schematics/scripts/generate_schematic_ai.py | 0 | create a high-quality scientific diagram with these requirements: visual quality: - clean white or light background (no |
| HIGH | …s/citation-management/scripts/generate_schematic_ai.py | 0 | create a high-quality scientific diagram with these requirements: visual quality: - clean white or light background (no |
| HIGH | skills/markitdown/scripts/generate_schematic_ai.py | 0 | create a high-quality scientific diagram with these requirements: visual quality: - clean white or light background (no |
| HIGH | skills/pptx-posters/scripts/generate_schematic_ai.py | 0 | create a high-quality scientific diagram with these requirements: visual quality: - clean white or light background (no |
| HIGH | skills/treatment-plans/scripts/generate_schematic_ai.py | 0 | create a high-quality scientific diagram with these requirements: visual quality: - clean white or light background (no |
| HIGH | …ls/scientific-writing/scripts/generate_schematic_ai.py | 0 | create a high-quality scientific diagram with these requirements: visual quality: - clean white or light background (no |
| HIGH | …ical-decision-support/scripts/generate_schematic_ai.py | 0 | create a high-quality scientific diagram with these requirements: visual quality: - clean white or light background (no |
| HIGH | …lls/literature-review/scripts/generate_schematic_ai.py | 0 | create a high-quality scientific diagram with these requirements: visual quality: - clean white or light background (no |
| HIGH | …ls/scholar-evaluation/scripts/generate_schematic_ai.py | 0 | create a high-quality scientific diagram with these requirements: visual quality: - clean white or light background (no |
| 261 more matches not shown… | |||
| Severity | File | Line | Snippet |
|---|---|---|---|
| LOW | scan_pr_skills.py | 63 | except Exception as exc: # pragma: no cover - defensive |
| LOW | scan_pr_skills.py | 84 | except Exception as exc: # pragma: no cover - defensive |
| LOW | scan_skills.py | 174 | except Exception as e: |
| LOW | scan_skills.py | 198 | except Exception as e: |
| LOW | …lls/benchling-integration/references/authentication.md | 328 | except Exception as e: |
| MEDIUM | skills/networkx/references/io.md | 431 | print(f"Error reading GraphML: {e}") |
| LOW | skills/research-lookup/research_lookup.py | 158 | except Exception as e: |
| LOW | skills/research-lookup/research_lookup.py | 285 | except Exception as e: |
| MEDIUM | skills/research-lookup/research_lookup.py | 489 | print("Error: No API keys found. Set at least one:", file=sys.stderr) |
| LOW | skills/research-lookup/research_lookup.py | 558 | except Exception as e: |
| MEDIUM | skills/research-lookup/research_lookup.py | 559 | print(f"Error: {e}", file=sys.stderr) |
| LOW | skills/research-lookup/lookup.py | 181 | except Exception as e: |
| MEDIUM | skills/research-lookup/scripts/generate_schematic_ai.py | 33 | print("Error: requests library not found. Install with: pip install requests") |
| LOW | skills/research-lookup/scripts/generate_schematic_ai.py | 288 | except Exception as e: |
| LOW | skills/research-lookup/scripts/generate_schematic_ai.py | 391 | except Exception as e: |
| LOW | skills/research-lookup/scripts/generate_schematic_ai.py | 548 | except Exception as e: |
| MEDIUM | skills/research-lookup/scripts/generate_schematic_ai.py | 782 | print("Error: OPENROUTER_API_KEY environment variable not set") |
| MEDIUM | skills/research-lookup/scripts/generate_schematic_ai.py | 790 | print("Error: Iterations must be between 1 and 2") |
| LOW | skills/research-lookup/scripts/generate_schematic_ai.py | 810 | except Exception as e: |
| MEDIUM | skills/research-lookup/scripts/generate_schematic.py | 95 | print("Error: OPENROUTER_API_KEY environment variable not set") |
| MEDIUM | skills/research-lookup/scripts/generate_schematic.py | 108 | print(f"Error: AI generation script not found: {ai_script}") |
| LOW | skills/research-lookup/scripts/generate_schematic.py | 132 | except Exception as e: |
| MEDIUM | skills/research-lookup/scripts/generate_schematic.py | 133 | print(f"Error executing AI generation: {e}") |
| LOW | skills/research-lookup/scripts/research_lookup.py | 158 | except Exception as e: |
| LOW | skills/research-lookup/scripts/research_lookup.py | 285 | except Exception as e: |
| MEDIUM | skills/research-lookup/scripts/research_lookup.py | 489 | print("Error: No API keys found. Set at least one:", file=sys.stderr) |
| LOW | skills/research-lookup/scripts/research_lookup.py | 558 | except Exception as e: |
| MEDIUM | skills/research-lookup/scripts/research_lookup.py | 559 | print(f"Error: {e}", file=sys.stderr) |
| MEDIUM | skills/shap/references/workflows.md | 70 | print(f"Error rate: {len(error_indices) / len(y_test):.2%}") |
| LOW | skills/dask/references/futures.md | 499 | except Exception as e: |
| LOW | skills/dask/references/futures.md | 533 | except Exception: |
| LOW | …ls/get-available-resources/scripts/detect_resources.py | 40 | except Exception: |
| LOW | …ls/get-available-resources/scripts/detect_resources.py | 75 | except Exception as e: |
| LOW | …ls/get-available-resources/scripts/detect_resources.py | 195 | except Exception: |
| LOW | …ls/get-available-resources/scripts/detect_resources.py | 199 | except Exception: |
| LOW | …ills/exploratory-data-analysis/scripts/eda_analyzer.py | 209 | except Exception as e: |
| MEDIUM | …ills/exploratory-data-analysis/scripts/eda_analyzer.py | 210 | print(f"Error loading reference: {e}", file=sys.stderr) |
| LOW | …ills/exploratory-data-analysis/scripts/eda_analyzer.py | 245 | except Exception as e: |
| LOW | …ills/exploratory-data-analysis/scripts/eda_analyzer.py | 329 | except Exception as e: |
| LOW | …ills/exploratory-data-analysis/scripts/eda_analyzer.py | 375 | except Exception as e: |
| LOW | …ills/exploratory-data-analysis/scripts/eda_analyzer.py | 415 | except Exception as e: |
| MEDIUM | …ills/exploratory-data-analysis/scripts/eda_analyzer.py | 529 | print(f"Error: File not found: {filepath}") |
| LOW | skills/iso-13485-certification/scripts/gap_analyzer.py | 217 | except Exception as e: |
| LOW | skills/esm/references/forge-api.md | 369 | except Exception as e: |
| MEDIUM | skills/esm/references/forge-api.md | 370 | print(f"Error processing {i}: {e}") |
| LOW | skills/esm/references/forge-api.md | 410 | except Exception as e: |
| LOW | skills/esm/references/forge-api.md | 588 | except Exception as e: |
| LOW | skills/esm/references/forge-api.md | 647 | except Exception as e: |
| MEDIUM | …scientific-schematics/scripts/generate_schematic_ai.py | 33 | print("Error: requests library not found. Install with: pip install requests") |
| LOW | …scientific-schematics/scripts/generate_schematic_ai.py | 288 | except Exception as e: |
| LOW | …scientific-schematics/scripts/generate_schematic_ai.py | 391 | except Exception as e: |
| LOW | …scientific-schematics/scripts/generate_schematic_ai.py | 548 | except Exception as e: |
| MEDIUM | …scientific-schematics/scripts/generate_schematic_ai.py | 782 | print("Error: OPENROUTER_API_KEY environment variable not set") |
| MEDIUM | …scientific-schematics/scripts/generate_schematic_ai.py | 790 | print("Error: Iterations must be between 1 and 2") |
| LOW | …scientific-schematics/scripts/generate_schematic_ai.py | 810 | except Exception as e: |
| MEDIUM | …ls/scientific-schematics/scripts/generate_schematic.py | 95 | print("Error: OPENROUTER_API_KEY environment variable not set") |
| MEDIUM | …ls/scientific-schematics/scripts/generate_schematic.py | 108 | print(f"Error: AI generation script not found: {ai_script}") |
| LOW | …ls/scientific-schematics/scripts/generate_schematic.py | 132 | except Exception as e: |
| MEDIUM | …ls/scientific-schematics/scripts/generate_schematic.py | 133 | print(f"Error executing AI generation: {e}") |
| LOW | skills/pyzotero/references/files-attachments.md | 95 | except Exception as e: |
| 587 more matches not shown… | |||
| Severity | File | Line | Snippet |
|---|---|---|---|
| MEDIUM | skills/pymc/references/workflows.md | 16 | # =============== |
| MEDIUM | skills/pymc/references/workflows.md | 24 | # ============== |
| MEDIUM | skills/pymc/references/workflows.md | 44 | # ========================== |
| MEDIUM | skills/pymc/references/workflows.md | 54 | # ============ |
| MEDIUM | skills/pymc/references/workflows.md | 70 | # ==================== |
| MEDIUM | skills/pymc/references/workflows.md | 92 | # ============================== |
| MEDIUM | skills/pymc/references/workflows.md | 102 | # ================== |
| MEDIUM | skills/pymc/references/workflows.md | 114 | # ============================ |
| MEDIUM | skills/pymc/references/workflows.md | 134 | # =============== |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 16 | # ============================================================================= |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 18 | # ============================================================================= |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 51 | # ============================================================================= |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 53 | # ============================================================================= |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 96 | # ============================================================================= |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 98 | # ============================================================================= |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 112 | # ============================================================================= |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 114 | # ============================================================================= |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 132 | # ============================================================================= |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 134 | # ============================================================================= |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 184 | # ============================================================================= |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 186 | # ============================================================================= |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 200 | # ============================================================================= |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 202 | # ============================================================================= |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 264 | # ============================================================================= |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 266 | # ============================================================================= |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 321 | # ============================================================================= |
| MEDIUM | skills/pymc/assets/hierarchical_model_template.py | 323 | # ============================================================================= |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 16 | # ============================================================================= |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 18 | # ============================================================================= |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 41 | # ============================================================================= |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 43 | # ============================================================================= |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 66 | # ============================================================================= |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 68 | # ============================================================================= |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 82 | # ============================================================================= |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 84 | # ============================================================================= |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 103 | # ============================================================================= |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 105 | # ============================================================================= |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 147 | # ============================================================================= |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 149 | # ============================================================================= |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 163 | # ============================================================================= |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 165 | # ============================================================================= |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 193 | # ============================================================================= |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 195 | # ============================================================================= |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 227 | # ============================================================================= |
| MEDIUM | skills/pymc/assets/linear_regression_template.py | 229 | # ============================================================================= |
| MEDIUM | skills/research-lookup/research_lookup.py | 101 | # ------------------------------------------------------------------ |
| MEDIUM | skills/research-lookup/research_lookup.py | 103 | # ------------------------------------------------------------------ |
| MEDIUM | skills/research-lookup/research_lookup.py | 197 | # ------------------------------------------------------------------ |
| MEDIUM | skills/research-lookup/research_lookup.py | 199 | # ------------------------------------------------------------------ |
| MEDIUM | skills/research-lookup/research_lookup.py | 295 | # ------------------------------------------------------------------ |
| MEDIUM | skills/research-lookup/research_lookup.py | 297 | # ------------------------------------------------------------------ |
| MEDIUM | skills/research-lookup/research_lookup.py | 404 | # ------------------------------------------------------------------ |
| MEDIUM | skills/research-lookup/research_lookup.py | 406 | # ------------------------------------------------------------------ |
| MEDIUM | skills/research-lookup/research_lookup.py | 434 | # --------------------------------------------------------------------------- |
| MEDIUM | skills/research-lookup/research_lookup.py | 436 | # --------------------------------------------------------------------------- |
| MEDIUM | skills/research-lookup/scripts/research_lookup.py | 101 | # ------------------------------------------------------------------ |
| MEDIUM | skills/research-lookup/scripts/research_lookup.py | 103 | # ------------------------------------------------------------------ |
| MEDIUM | skills/research-lookup/scripts/research_lookup.py | 197 | # ------------------------------------------------------------------ |
| MEDIUM | skills/research-lookup/scripts/research_lookup.py | 199 | # ------------------------------------------------------------------ |
| MEDIUM | skills/research-lookup/scripts/research_lookup.py | 295 | # ------------------------------------------------------------------ |
| 106 more matches not shown… | |||
| Severity | File | Line | Snippet |
|---|---|---|---|
| LOW | skills/qiskit/references/patterns.md | 449 | def cost_function_with_tracking(params): |
| LOW | skills/pymc/scripts/model_comparison.py | 291 | def cross_validation_comparison(models_dict: Dict[str, az.InferenceData], |
| LOW | skills/research-lookup/research_lookup.py | 370 | def _extract_citations_from_text(self, text: str) -> List[Dict[str, str]]: |
| LOW | skills/research-lookup/examples.py | 16 | def example_automatic_selection(): |
| LOW | skills/research-lookup/examples.py | 96 | def example_scientific_writing_workflow(): |
| LOW | skills/research-lookup/scripts/generate_schematic_ai.py | 214 | def _extract_image_from_response(self, response: Dict[str, Any]) -> Optional[bytes]: |
| LOW | skills/research-lookup/scripts/research_lookup.py | 370 | def _extract_citations_from_text(self, text: str) -> List[Dict[str, str]]: |
| LOW | skills/geomaster/references/scientific-domains.md | 14 | def coastal_vulnerability_index(dem_path, shoreline_path, output_path): |
| LOW | skills/geomaster/references/scientific-domains.md | 350 | def estimate_biomass_from_lidar(chm_path, plot_data): |
| LOW | skills/geomaster/references/industry-applications.md | 221 | def power_line_corridor_analysis(power_lines_path, vegetation_height_path, buffer_distance=50): |
| LOW | skills/geomaster/references/advanced-gis.md | 176 | def emerging_hot_spot_analysis(cube, k=8): |
| LOW | skills/geomaster/references/machine-learning.md | 18 | def train_random_forest_classifier(raster_path, training_gdf): |
| LOW | skills/dask/references/dataframes.md | 140 | def custom_partition_function(partition_df): |
| LOW | …ills/exploratory-data-analysis/scripts/eda_analyzer.py | 251 | def analyze_general_scientific(filepath, extension): |
| LOW | skills/iso-13485-certification/scripts/gap_analyzer.py | 291 | def _generate_recommendations(self, missing_procedures: List[Dict], |
| LOW | skills/esm/references/workflows.md | 475 | def predict_function_generative(sequence): |
| LOW | skills/esm/references/workflows.md | 491 | def predict_function_embedding(sequence, function_classifier): |
| LOW | skills/esm/references/esm3-api.md | 318 | def generate_with_temperature_schedule(model, protein, temperatures): |
| LOW | skills/esm/references/esm-c-api.md | 127 | def batch_encode_variable_length(model, sequences, max_batch_size=32): |
| LOW | skills/esm/references/esm-c-api.md | 364 | def get_per_residue_embeddings(model, sequence): |
| LOW | skills/esm/references/esm-c-api.md | 410 | def efficient_batch_processing(model, sequences, batch_size=32): |
| LOW | …scientific-schematics/scripts/generate_schematic_ai.py | 214 | def _extract_image_from_response(self, response: Dict[str, Any]) -> Optional[bytes]: |
| LOW | skills/deeptools/scripts/workflow_generator.py | 32 | def generate_chipseq_qc_workflow(output_file, params): |
| LOW | skills/deeptools/scripts/workflow_generator.py | 107 | def generate_chipseq_analysis_workflow(output_file, params): |
| LOW | skills/deeptools/scripts/workflow_generator.py | 226 | def generate_rnaseq_coverage_workflow(output_file, params): |
| LOW | skills/deeptools/scripts/workflow_generator.py | 275 | def generate_atacseq_workflow(output_file, params): |
| LOW | skills/fluidsim/references/advanced_features.md | 291 | def _complete_params_with_default(params): |
| LOW | …s/citation-management/scripts/generate_schematic_ai.py | 214 | def _extract_image_from_response(self, response: Dict[str, Any]) -> Optional[bytes]: |
| LOW | skills/citation-management/scripts/search_pubmed.py | 154 | def _extract_metadata_from_xml(self, article: ET.Element) -> Optional[Dict]: |
| LOW | skills/markitdown/scripts/generate_schematic_ai.py | 214 | def _extract_image_from_response(self, response: Dict[str, Any]) -> Optional[bytes]: |
| LOW | skills/markitdown/scripts/convert_literature.py | 19 | def extract_metadata_from_filename(filename: str) -> Dict[str, str]: |
| LOW | skills/pytdc/scripts/benchmark_evaluation.py | 43 | def single_dataset_evaluation(group, dataset_name='Caco2_Wang'): |
| LOW | skills/pytdc/scripts/benchmark_evaluation.py | 102 | def multiple_datasets_evaluation(group): |
| LOW | skills/pytdc/scripts/benchmark_evaluation.py | 247 | def leaderboard_submission_guide(): |
| LOW | skills/pytdc/scripts/molecular_generation.py | 156 | def goal_directed_generation_template(): |
| LOW | skills/pytdc/scripts/molecular_generation.py | 220 | def distribution_learning_example(train_smiles): |
| LOW | skills/pytdc/scripts/molecular_generation.py | 309 | def constraint_satisfaction_example(): |
| LOW | skills/xlsx/scripts/office/validators/docx.py | 66 | def validate_whitespace_preservation(self): |
| LOW | skills/xlsx/scripts/office/validators/docx.py | 163 | def count_paragraphs_in_unpacked(self): |
| LOW | skills/xlsx/scripts/office/validators/docx.py | 179 | def count_paragraphs_in_original(self): |
| LOW | skills/xlsx/scripts/office/validators/redlining.py | 198 | def _remove_author_tracked_changes(self, root): |
| LOW | skills/xlsx/scripts/office/validators/pptx.py | 104 | def validate_slide_layout_ids(self): |
| LOW | skills/xlsx/scripts/office/validators/pptx.py | 172 | def validate_no_duplicate_slide_layouts(self): |
| LOW | skills/xlsx/scripts/office/validators/pptx.py | 210 | def validate_notes_slide_references(self): |
| LOW | skills/xlsx/scripts/office/validators/base.py | 115 | def repair_whitespace_preservation(self) -> int: |
| LOW | skills/xlsx/scripts/office/validators/base.py | 385 | def validate_all_relationship_ids(self): |
| LOW | skills/xlsx/scripts/office/validators/base.py | 469 | def _get_expected_relationship_type(self, element_name): |
| LOW | skills/xlsx/scripts/office/validators/base.py | 598 | def validate_file_against_xsd(self, xml_file, verbose=False): |
| LOW | skills/xlsx/scripts/office/validators/base.py | 703 | def _clean_ignorable_namespaces(self, xml_doc): |
| LOW | skills/xlsx/scripts/office/validators/base.py | 723 | def _remove_ignorable_elements(self, root): |
| LOW | skills/xlsx/scripts/office/validators/base.py | 742 | def _preprocess_for_mc_ignorable(self, xml_doc): |
| LOW | skills/xlsx/scripts/office/validators/base.py | 750 | def _validate_single_file_xsd(self, xml_file, base_path): |
| LOW | skills/xlsx/scripts/office/validators/base.py | 787 | def _get_original_file_errors(self, xml_file): |
| LOW | skills/xlsx/scripts/office/validators/base.py | 814 | def _remove_template_tags_from_text_nodes(self, xml_doc): |
| LOW | skills/xlsx/scripts/office/helpers/simplify_redlines.py | 47 | def _merge_tracked_changes_in(container, tag: str) -> int: |
| LOW | skills/xlsx/scripts/office/helpers/simplify_redlines.py | 126 | def get_tracked_change_authors(doc_xml_path: Path) -> dict[str, int]: |
| LOW | skills/pdf/scripts/fill_fillable_fields.py | 55 | def validation_error_for_field_value(field_info, field_value): |
| LOW | skills/pdf/scripts/extract_form_field_info.py | 9 | def get_full_annotation_field_id(annotation): |
| LOW | skills/pdf/scripts/check_bounding_boxes.py | 15 | def get_bounding_box_messages(fields_json_stream) -> list[str]: |
| LOW | skills/pdf/scripts/fill_pdf_form_with_annotations.py | 10 | def transform_from_image_coords(bbox, image_width, image_height, pdf_width, pdf_height): |
| 278 more matches not shown… | |||
| Severity | File | Line | Snippet |
|---|---|---|---|
| HIGH | SECURITY.md | 1699 | > Several code examples contain placeholder API keys and credentials (e.g., YOUR_API_KEY, YOUR_ACCESS_TOKEN, 'user'/'p |
| HIGH | SECURITY.md | 3293 | > The references/AI_CURATION.md and SKILL.md show API client instantiation with api_key parameters passed directly (e. |
| HIGH | SECURITY.md | 3403 | > The devices_backends.md reference file includes code examples that show API tokens being passed as string literals ( |
| HIGH | …lls/benchling-integration/references/authentication.md | 301 | -u "your_api_key:" \ |
| HIGH | …lls/benchling-integration/references/authentication.md | 321 | auth_method=ApiKeyAuth("your_api_key") |
| HIGH | …lls/benchling-integration/references/authentication.md | 381 | auth_method=ApiKeyAuth("your_api_key"), |
| HIGH | …ills/benchling-integration/references/api_endpoints.md | 26 | -u "your_api_key:" |
| HIGH | …ills/benchling-integration/references/sdk_reference.md | 571 | auth_method=ApiKeyAuth("your_api_key"), |
| HIGH | …ills/benchling-integration/references/sdk_reference.md | 578 | auth_method=ApiKeyAuth("your_api_key"), |
| HIGH | skills/research-lookup/scripts/generate_schematic_ai.py | 784 | print(" export OPENROUTER_API_KEY='your_api_key'") |
| HIGH | skills/research-lookup/scripts/generate_schematic.py | 99 | print(" export OPENROUTER_API_KEY='your_api_key'") |
| HIGH | skills/geomaster/references/data-sources.md | 179 | 'key': YOUR_API_KEY |
| HIGH | skills/geomaster/references/data-sources.md | 208 | 'appid': YOUR_API_KEY |
| HIGH | …scientific-schematics/scripts/generate_schematic_ai.py | 784 | print(" export OPENROUTER_API_KEY='your_api_key'") |
| HIGH | …ls/scientific-schematics/scripts/generate_schematic.py | 99 | print(" export OPENROUTER_API_KEY='your_api_key'") |
| HIGH | skills/pyzotero/SKILL.md | 28 | ZOTERO_API_KEY=your_api_key |
| HIGH | skills/database-lookup/references/bea.md | 13 | - Pass as query parameter: `&UserID=YOUR_API_KEY` |
| HIGH | skills/database-lookup/references/lincs-l1000.md | 13 | - Pass via header: `user_key: YOUR_API_KEY` |
| HIGH | skills/database-lookup/references/lincs-l1000.md | 36 | curl -H "user_key: YOUR_API_KEY" \ |
| HIGH | skills/database-lookup/references/lincs-l1000.md | 40 | curl -H "user_key: YOUR_API_KEY" \ |
| HIGH | skills/database-lookup/references/lincs-l1000.md | 44 | curl -H "user_key: YOUR_API_KEY" \ |
| HIGH | skills/database-lookup/references/lincs-l1000.md | 48 | curl -H "user_key: YOUR_API_KEY" \ |
| HIGH | skills/database-lookup/references/omim.md | 10 | - Pass as query parameter: `?apiKey=YOUR_API_KEY` |
| HIGH | skills/database-lookup/references/addgene.md | 10 | Pass as: `Authorization: Token <your_api_key>` |
| HIGH | skills/citation-management/references/pubmed_search.md | 385 | api_key=YOUR_API_KEY |
| HIGH | skills/citation-management/references/pubmed_search.md | 418 | api_key=YOUR_API_KEY |
| HIGH | skills/citation-management/references/pubmed_search.md | 442 | api_key=YOUR_API_KEY |
| HIGH | …s/citation-management/scripts/generate_schematic_ai.py | 784 | print(" export OPENROUTER_API_KEY='your_api_key'") |
| HIGH | …ills/citation-management/scripts/generate_schematic.py | 99 | print(" export OPENROUTER_API_KEY='your_api_key'") |
| HIGH | skills/markitdown/scripts/generate_schematic_ai.py | 784 | print(" export OPENROUTER_API_KEY='your_api_key'") |
| HIGH | skills/markitdown/scripts/generate_schematic.py | 99 | print(" export OPENROUTER_API_KEY='your_api_key'") |
| HIGH | skills/infographics/scripts/generate_infographic_ai.py | 1286 | print(" export OPENROUTER_API_KEY='your_api_key'") |
| HIGH | skills/infographics/scripts/generate_infographic.py | 182 | print(" export OPENROUTER_API_KEY='your_api_key'") |
| HIGH | skills/pptx-posters/scripts/generate_schematic_ai.py | 784 | print(" export OPENROUTER_API_KEY='your_api_key'") |
| HIGH | skills/pptx-posters/scripts/generate_schematic.py | 99 | print(" export OPENROUTER_API_KEY='your_api_key'") |
| HIGH | skills/treatment-plans/scripts/generate_schematic_ai.py | 784 | print(" export OPENROUTER_API_KEY='your_api_key'") |
| HIGH | skills/treatment-plans/scripts/generate_schematic.py | 99 | print(" export OPENROUTER_API_KEY='your_api_key'") |
| HIGH | …ls/scientific-writing/scripts/generate_schematic_ai.py | 784 | print(" export OPENROUTER_API_KEY='your_api_key'") |
| HIGH | skills/scientific-writing/scripts/generate_schematic.py | 99 | print(" export OPENROUTER_API_KEY='your_api_key'") |
| HIGH | skills/scientific-writing/scripts/generate_image.py | 108 | print("OPENROUTER_API_KEY=your-api-key-here") |
| HIGH | skills/scientific-writing/scripts/generate_image.py | 110 | print("export OPENROUTER_API_KEY=your-api-key-here") |
| HIGH | …ical-decision-support/scripts/generate_schematic_ai.py | 784 | print(" export OPENROUTER_API_KEY='your_api_key'") |
| HIGH | …linical-decision-support/scripts/generate_schematic.py | 99 | print(" export OPENROUTER_API_KEY='your_api_key'") |
| HIGH | skills/paper-lookup/references/core.md | 15 | - **Header:** `Authorization: Bearer YOUR_API_KEY` |
| HIGH | skills/paper-lookup/references/core.md | 16 | - **Query param:** `?api_key=YOUR_API_KEY` |
| HIGH | …lls/literature-review/scripts/generate_schematic_ai.py | 784 | print(" export OPENROUTER_API_KEY='your_api_key'") |
| HIGH | skills/literature-review/scripts/generate_schematic.py | 99 | print(" export OPENROUTER_API_KEY='your_api_key'") |
| HIGH | …ls/scholar-evaluation/scripts/generate_schematic_ai.py | 784 | print(" export OPENROUTER_API_KEY='your_api_key'") |
| HIGH | skills/scholar-evaluation/scripts/generate_schematic.py | 99 | print(" export OPENROUTER_API_KEY='your_api_key'") |
| HIGH | skills/cirq/references/hardware.md | 173 | # export IONQ_API_KEY=your_api_key |
| HIGH | skills/cirq/references/hardware.md | 493 | export IONQ_API_KEY=your_api_key |
| HIGH | skills/latex-posters/scripts/generate_schematic_ai.py | 784 | print(" export OPENROUTER_API_KEY='your_api_key'") |
| HIGH | skills/latex-posters/scripts/generate_schematic.py | 99 | print(" export OPENROUTER_API_KEY='your_api_key'") |
| HIGH | skills/adaptyv/SKILL.md | 53 | ADAPTYV_API_KEY=your_api_key |
| HIGH | skills/venue-templates/scripts/generate_schematic_ai.py | 784 | print(" export OPENROUTER_API_KEY='your_api_key'") |
| HIGH | skills/venue-templates/scripts/generate_schematic.py | 99 | print(" export OPENROUTER_API_KEY='your_api_key'") |
| HIGH | skills/pytorch-lightning/references/logging.md | 103 | api_key="YOUR_API_KEY", |
| HIGH | …ills/clinical-reports/scripts/generate_schematic_ai.py | 784 | print(" export OPENROUTER_API_KEY='your_api_key'") |
| HIGH | skills/clinical-reports/scripts/generate_schematic.py | 99 | print(" export OPENROUTER_API_KEY='your_api_key'") |
| HIGH | …lls/scientific-slides/scripts/generate_schematic_ai.py | 784 | print(" export OPENROUTER_API_KEY='your_api_key'") |
| 14 more matches not shown… | |||
| Severity | File | Line | Snippet |
|---|---|---|---|
| HIGH | skills/xlsx/scripts/office/soffice.py | 150 | if (sv[0] >= 0 && sv[0] < 1024) { |
| HIGH | skills/xlsx/scripts/office/soffice.py | 169 | if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) { |
| HIGH | skills/xlsx/scripts/office/soffice.py | 178 | if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) { |
| HIGH | skills/xlsx/scripts/office/soffice.py | 192 | if (fd >= 0 && fd < 1024 && is_shimmed[fd]) { |
| HIGH | …recasting/examples/global-temperature/generate_html.py | 403 | ...Array(nActual).fill(null), |
| HIGH | …recasting/examples/global-temperature/generate_html.py | 411 | dataUsed.push(step.historical_values[i]); |
| HIGH | …recasting/examples/global-temperature/generate_html.py | 413 | dataUsed.push(null); |
| HIGH | …recasting/examples/global-temperature/generate_html.py | 413 | dataUsed.push(null); |
| HIGH | …recasting/examples/global-temperature/generate_html.py | 427 | if (forecastIdx >= 0 && forecastIdx < nForecast) {{ |
| HIGH | …recasting/examples/global-temperature/generate_html.py | 428 | q90Lower.push(step.q10[forecastIdx]); |
| HIGH | …recasting/examples/global-temperature/generate_html.py | 429 | q90Upper.push(step.q90[forecastIdx]); |
| HIGH | …recasting/examples/global-temperature/generate_html.py | 430 | q80Lower.push(step.q20[forecastIdx]); |
| HIGH | …recasting/examples/global-temperature/generate_html.py | 431 | q80Upper.push(step.q80[forecastIdx]); |
| HIGH | …recasting/examples/global-temperature/generate_html.py | 433 | q90Lower.push(null); |
| HIGH | …recasting/examples/global-temperature/generate_html.py | 433 | q90Lower.push(null); |
| HIGH | …recasting/examples/global-temperature/generate_html.py | 434 | q90Upper.push(null); |
| HIGH | …recasting/examples/global-temperature/generate_html.py | 434 | q90Upper.push(null); |
| HIGH | …recasting/examples/global-temperature/generate_html.py | 435 | q80Lower.push(null); |
| HIGH | …recasting/examples/global-temperature/generate_html.py | 435 | q80Lower.push(null); |
| HIGH | …recasting/examples/global-temperature/generate_html.py | 436 | q80Upper.push(null); |
| HIGH | …recasting/examples/global-temperature/generate_html.py | 436 | q80Upper.push(null); |
| HIGH | …recasting/examples/global-temperature/generate_html.py | 448 | if (forecastIdx >= 0 && forecastIdx < nForecast) {{ |
| HIGH | …recasting/examples/global-temperature/generate_html.py | 449 | forecastData.push(step.point_forecast[forecastIdx]); |
| HIGH | …recasting/examples/global-temperature/generate_html.py | 451 | forecastData.push(null); |
| HIGH | …recasting/examples/global-temperature/generate_html.py | 451 | forecastData.push(null); |
| HIGH | …recasting/examples/global-temperature/generate_html.py | 227 | let chart = null; |
| HIGH | …recasting/examples/global-temperature/generate_html.py | 229 | let playInterval = null; |
| HIGH | …recasting/examples/global-temperature/generate_html.py | 275 | data: [...Array(animationData.actual_data.dates.length).fill(null), ...finalStep.point_forec |
| HIGH | skills/treatment-plans/scripts/check_completeness.py | 257 | python check_completeness.py plan.tex && echo "Complete" |
| HIGH | …lls/treatment-plans/scripts/validate_treatment_plan.py | 313 | python validate_treatment_plan.py plan.tex && echo "Quality check passed" |
| HIGH | skills/pptx/scripts/office/soffice.py | 116 | if (sv[0] >= 0 && sv[0] < 1024) { |
| HIGH | skills/pptx/scripts/office/soffice.py | 135 | if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) { |
| HIGH | skills/pptx/scripts/office/soffice.py | 144 | if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) { |
| HIGH | skills/pptx/scripts/office/soffice.py | 158 | if (fd >= 0 && fd < 1024 && is_shimmed[fd]) { |
| HIGH | skills/docx/scripts/office/soffice.py | 116 | if (sv[0] >= 0 && sv[0] < 1024) { |
| HIGH | skills/docx/scripts/office/soffice.py | 135 | if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) { |
| HIGH | skills/docx/scripts/office/soffice.py | 144 | if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) { |
| HIGH | skills/docx/scripts/office/soffice.py | 158 | if (fd >= 0 && fd < 1024 && is_shimmed[fd]) { |
| Severity | File | Line | Snippet |
|---|---|---|---|
| LOW | scan_pr_skills.py | 99 | |
| LOW | scan_skills.py | 58 | |
| LOW | skills/pymc/scripts/model_comparison.py | 27 | |
| LOW | skills/pymc/scripts/model_comparison.py | 120 | |
| LOW | skills/research-lookup/research_lookup.py | 438 | |
| LOW | skills/research-lookup/research_lookup.py | 168 | |
| LOW | skills/research-lookup/scripts/generate_schematic_ai.py | 214 | |
| LOW | skills/research-lookup/scripts/generate_schematic_ai.py | 321 | |
| LOW | skills/research-lookup/scripts/generate_schematic_ai.py | 399 | |
| LOW | skills/research-lookup/scripts/research_lookup.py | 438 | |
| LOW | skills/research-lookup/scripts/research_lookup.py | 168 | |
| LOW | …ls/get-available-resources/scripts/detect_resources.py | 82 | |
| LOW | …ls/get-available-resources/scripts/detect_resources.py | 117 | |
| LOW | …ls/get-available-resources/scripts/detect_resources.py | 150 | |
| LOW | …ls/get-available-resources/scripts/detect_resources.py | 274 | |
| LOW | …ills/exploratory-data-analysis/scripts/eda_analyzer.py | 215 | |
| LOW | …ills/exploratory-data-analysis/scripts/eda_analyzer.py | 251 | |
| LOW | …ills/exploratory-data-analysis/scripts/eda_analyzer.py | 335 | |
| LOW | …ills/exploratory-data-analysis/scripts/eda_analyzer.py | 381 | |
| LOW | skills/iso-13485-certification/scripts/gap_analyzer.py | 197 | |
| LOW | …scientific-schematics/scripts/generate_schematic_ai.py | 214 | |
| LOW | …scientific-schematics/scripts/generate_schematic_ai.py | 321 | |
| LOW | …scientific-schematics/scripts/generate_schematic_ai.py | 399 | |
| LOW | skills/deeptools/scripts/validate_files.py | 46 | |
| LOW | skills/deeptools/scripts/workflow_generator.py | 361 | |
| LOW | skills/medchem/scripts/filter_molecules.py | 28 | |
| LOW | skills/pymatgen/scripts/structure_analyzer.py | 36 | |
| LOW | skills/pymatgen/scripts/structure_analyzer.py | 194 | |
| LOW | skills/pymatgen/scripts/structure_converter.py | 87 | |
| LOW | skills/pymatgen/scripts/phase_diagram_generator.py | 48 | |
| LOW | skills/citation-management/scripts/extract_metadata.py | 141 | |
| LOW | skills/citation-management/scripts/extract_metadata.py | 213 | |
| LOW | …s/citation-management/scripts/generate_schematic_ai.py | 214 | |
| LOW | …s/citation-management/scripts/generate_schematic_ai.py | 321 | |
| LOW | …s/citation-management/scripts/generate_schematic_ai.py | 399 | |
| LOW | skills/citation-management/scripts/format_bibtex.py | 201 | |
| LOW | skills/citation-management/scripts/format_bibtex.py | 213 | |
| LOW | …s/citation-management/scripts/search_google_scholar.py | 47 | |
| LOW | …ills/citation-management/scripts/validate_citations.py | 95 | |
| LOW | …ills/citation-management/scripts/validate_citations.py | 303 | |
| LOW | skills/citation-management/scripts/search_pubmed.py | 98 | |
| LOW | skills/citation-management/scripts/search_pubmed.py | 154 | |
| LOW | skills/pydicom/scripts/anonymize_dicom.py | 40 | |
| LOW | skills/pydicom/scripts/dicom_to_image.py | 52 | |
| LOW | skills/markitdown/scripts/generate_schematic_ai.py | 214 | |
| LOW | skills/markitdown/scripts/generate_schematic_ai.py | 321 | |
| LOW | skills/markitdown/scripts/generate_schematic_ai.py | 399 | |
| LOW | skills/xlsx/scripts/recalc.py | 73 | |
| LOW | skills/xlsx/scripts/office/pack.py | 24 | |
| LOW | skills/xlsx/scripts/office/pack.py | 108 | |
| LOW | skills/xlsx/scripts/office/validators/docx.py | 66 | |
| LOW | skills/xlsx/scripts/office/validators/docx.py | 112 | |
| LOW | skills/xlsx/scripts/office/validators/docx.py | 254 | |
| LOW | skills/xlsx/scripts/office/validators/docx.py | 298 | |
| LOW | skills/xlsx/scripts/office/validators/docx.py | 391 | |
| LOW | skills/xlsx/scripts/office/validators/redlining.py | 127 | |
| LOW | skills/xlsx/scripts/office/validators/redlining.py | 198 | |
| LOW | skills/xlsx/scripts/office/validators/pptx.py | 62 | |
| LOW | skills/xlsx/scripts/office/validators/pptx.py | 104 | |
| LOW | skills/xlsx/scripts/office/validators/pptx.py | 210 | |
| 170 more matches not shown… | |||
| Severity | File | Line | Snippet |
|---|---|---|---|
| LOW | skills/deeptools/scripts/workflow_generator.py | 51 | # Step 1: Correlation analysis |
| LOW | skills/deeptools/scripts/workflow_generator.py | 72 | # Step 2: Coverage assessment |
| LOW | skills/deeptools/scripts/workflow_generator.py | 80 | # Step 3: Fragment size (for paired-end data) |
| LOW | skills/deeptools/scripts/workflow_generator.py | 87 | # Step 4: ChIP signal strength |
| LOW | skills/deeptools/scripts/workflow_generator.py | 128 | # Step 1: Generate normalized coverage tracks |
| LOW | skills/deeptools/scripts/workflow_generator.py | 151 | # Step 2: Create log2 ratio track |
| LOW | skills/deeptools/scripts/workflow_generator.py | 164 | # Step 3: Compute matrix around TSS |
| LOW | skills/deeptools/scripts/workflow_generator.py | 178 | # Step 4: Generate heatmap |
| LOW | skills/deeptools/scripts/workflow_generator.py | 191 | # Step 5: Generate profile plot |
| LOW | skills/deeptools/scripts/workflow_generator.py | 203 | # Step 6: Enrichment at peaks (if peaks provided) |
| LOW | skills/deeptools/scripts/workflow_generator.py | 294 | # Step 1: Shift reads for Tn5 correction |
| LOW | skills/deeptools/scripts/workflow_generator.py | 307 | # Step 2: Generate coverage track |
| LOW | skills/deeptools/scripts/workflow_generator.py | 317 | # Step 3: Fragment size analysis |
| LOW | skills/deeptools/scripts/workflow_generator.py | 324 | # Step 4: Compute matrix at peaks (if peaks provided) |
| LOW | …forecasting/examples/global-temperature/run_example.sh | 26 | # Step 1: Preflight check |
| LOW | …forecasting/examples/global-temperature/run_example.sh | 34 | # Step 2: Run forecast |
| LOW | …forecasting/examples/global-temperature/run_example.sh | 40 | # Step 3: Generate visualization |
| LOW | …ls/opentrons-integration/scripts/pcr_setup_template.py | 80 | # Step 1: Distribute master mix |
| LOW | …ls/opentrons-integration/scripts/pcr_setup_template.py | 90 | # Step 2: Add template DNA |
| LOW | …ntrons-integration/scripts/serial_dilution_template.py | 65 | # Step 1: Add diluent to all wells except first column |
| LOW | …ntrons-integration/scripts/serial_dilution_template.py | 75 | # Step 2: Add stock solution to first column |
| LOW | …ntrons-integration/scripts/serial_dilution_template.py | 84 | # Step 3: Perform serial dilution |
| LOW | skills/bioservices/scripts/compound_cross_reference.py | 337 | # Step 1: Search KEGG |
| LOW | skills/bioservices/scripts/compound_cross_reference.py | 343 | # Step 2: Get KEGG details |
| LOW | skills/bioservices/scripts/compound_cross_reference.py | 346 | # Step 3: Map to ChEMBL |
| LOW | skills/bioservices/scripts/compound_cross_reference.py | 349 | # Step 4: Get ChEBI details |
| LOW | skills/bioservices/scripts/compound_cross_reference.py | 354 | # Step 5: Get ChEMBL details |
| LOW | skills/bioservices/scripts/protein_analysis_workflow.py | 388 | # Step 1: Search protein |
| LOW | skills/bioservices/scripts/protein_analysis_workflow.py | 394 | # Step 2: Retrieve sequence |
| LOW | skills/bioservices/scripts/protein_analysis_workflow.py | 399 | # Step 3: BLAST search |
| LOW | skills/bioservices/scripts/protein_analysis_workflow.py | 404 | # Step 4: Pathway discovery |
| LOW | skills/bioservices/scripts/protein_analysis_workflow.py | 408 | # Step 5: Interaction mapping |
| LOW | skills/bioservices/scripts/protein_analysis_workflow.py | 411 | # Step 6: GO annotations |
| LOW | skills/gget/scripts/batch_sequence_analysis.py | 67 | # Step 1: BLAST each sequence |
| LOW | skills/gget/scripts/batch_sequence_analysis.py | 90 | # Step 2: Multiple sequence alignment |
| LOW | skills/gget/scripts/batch_sequence_analysis.py | 105 | # Step 3: Structure prediction (optional) |
| LOW | skills/gget/scripts/gene_analysis.py | 27 | # Step 1: Search for the gene |
| LOW | skills/gget/scripts/gene_analysis.py | 39 | # Step 2: Get detailed information |
| LOW | skills/gget/scripts/gene_analysis.py | 50 | # Step 3: Get sequences |
| LOW | skills/gget/scripts/gene_analysis.py | 63 | # Step 4: Get tissue expression |
| LOW | skills/gget/scripts/gene_analysis.py | 78 | # Step 5: Find correlated genes |
| LOW | skills/gget/scripts/gene_analysis.py | 92 | # Step 6: Get disease associations |
| LOW | skills/gget/scripts/gene_analysis.py | 105 | # Step 7: Get drug associations |
| LOW | …s/neuropixels-analysis/scripts/neuropixels_pipeline.py | 63 | # Step 1: High-pass filter |
| LOW | …s/neuropixels-analysis/scripts/neuropixels_pipeline.py | 67 | # Step 2: Detect bad channels |
| LOW | …s/neuropixels-analysis/scripts/neuropixels_pipeline.py | 75 | # Step 3: Phase shift (for Neuropixels 1.0) |
| LOW | …s/neuropixels-analysis/scripts/neuropixels_pipeline.py | 80 | # Step 4: Common median reference |
| LOW | skills/pymoo/scripts/decision_making_example.py | 138 | # Step 1: Run optimization |
| LOW | skills/pymoo/scripts/decision_making_example.py | 141 | # Step 2: Find extreme solutions |
| LOW | skills/pymoo/scripts/decision_making_example.py | 144 | # Step 3: Compare different preference weights |
| LOW | skills/pymoo/scripts/decision_making_example.py | 147 | # Step 4: Visualize selections with petal diagram |
| LOW | skills/phylogenetics/scripts/phylogenetic_analysis.py | 234 | # Step 1: Multiple Sequence Alignment |
| LOW | skills/phylogenetics/scripts/phylogenetic_analysis.py | 243 | # Step 2: Tree Inference |
| LOW | skills/phylogenetics/scripts/phylogenetic_analysis.py | 256 | # Step 3: Visualization |
| Severity | File | Line | Snippet |
|---|---|---|---|
| LOW | scan_pr_skills.py | 15 | |
| LOW | skills/pymc/scripts/model_comparison.py | 22 | |
| LOW | skills/pymc/assets/hierarchical_model_template.py | 13 | |
| LOW | skills/pymc/assets/linear_regression_template.py | 13 | |
| LOW | skills/research-lookup/lookup.py | 9 | |
| LOW | skills/research-lookup/lookup.py | 10 | |
| LOW | …ls/get-available-resources/scripts/detect_resources.py | 19 | |
| LOW | …ls/get-available-resources/scripts/detect_resources.py | 20 | |
| LOW | skills/iso-13485-certification/scripts/gap_analyzer.py | 16 | |
| LOW | skills/deeptools/scripts/validate_files.py | 12 | |
| LOW | skills/medchem/scripts/filter_molecules.py | 14 | |
| LOW | skills/pymatgen/scripts/structure_analyzer.py | 25 | |
| LOW | skills/pathway-enrichment/scripts/run_enrichment.py | 29 | |
| LOW | skills/citation-management/scripts/format_bibtex.py | 10 | |
| LOW | skills/markitdown/scripts/convert_literature.py | 14 | |
| LOW | skills/pytdc/scripts/load_and_split_data.py | 15 | |
| LOW | skills/xlsx/scripts/office/validators/__init__.py | 5 | |
| LOW | skills/xlsx/scripts/office/validators/__init__.py | 6 | |
| LOW | skills/xlsx/scripts/office/validators/__init__.py | 7 | |
| LOW | skills/xlsx/scripts/office/validators/__init__.py | 8 | |
| LOW | skills/exa-search/tests/test_exa_search.py | 12 | |
| LOW | skills/exa-search/scripts/exa_search.py | 16 | |
| LOW | skills/exa-search/scripts/exa_extract.py | 15 | |
| LOW | skills/autoskill/tests/test_e2e.py | 9 | |
| LOW | …ing/examples/covariates-forecasting/demo_covariates.py | 28 | |
| LOW | …casting/examples/anomaly-detection/detect_anomalies.py | 17 | |
| LOW | …orecasting/examples/global-temperature/run_forecast.py | 7 | |
| LOW | …recasting/examples/global-temperature/generate_html.py | 9 | |
| LOW | …ting/examples/global-temperature/visualize_forecast.py | 14 | |
| LOW | …examples/global-temperature/generate_animation_data.py | 11 | |
| LOW | …orecasting/examples/global-temperature/generate_gif.py | 8 | |
| LOW | skills/timesfm-forecasting/scripts/forecast_csv.py | 21 | |
| LOW | skills/timesfm-forecasting/scripts/check_system.py | 16 | |
| LOW | …ills/statistical-analysis/scripts/assumption_checks.py | 16 | |
| LOW | …ills/statistical-analysis/scripts/assumption_checks.py | 17 | |
| LOW | …ical-decision-support/scripts/validate_cds_document.py | 19 | |
| LOW | …inical-decision-support/scripts/build_decision_tree.py | 12 | |
| LOW | skills/diffdock/scripts/analyze_results.py | 17 | |
| LOW | skills/diffdock/scripts/analyze_results.py | 19 | |
| LOW | skills/pydeseq2/scripts/run_deseq2_analysis.py | 20 | |
| LOW | skills/literature-review/scripts/verify_citations.py | 11 | |
| LOW | skills/scholar-evaluation/scripts/calculate_scores.py | 20 | |
| LOW | skills/pptx/scripts/office/validators/__init__.py | 5 | |
| LOW | skills/pptx/scripts/office/validators/__init__.py | 6 | |
| LOW | skills/pptx/scripts/office/validators/__init__.py | 7 | |
| LOW | skills/pptx/scripts/office/validators/__init__.py | 8 | |
| LOW | skills/primekg/scripts/query_primekg.py | 3 | |
| LOW | …ills/open-notebook/scripts/test_open_notebook_skill.py | 11 | |
| LOW | …et-research-reports/scripts/generate_market_visuals.py | 23 | |
| LOW | skills/deepchem/scripts/predict_solubility.py | 15 | |
| LOW | skills/scvelo/scripts/rna_velocity_workflow.py | 14 | |
| LOW | skills/scvelo/scripts/rna_velocity_workflow.py | 17 | |
| LOW | skills/simpy/scripts/resource_monitor.py | 11 | |
| LOW | skills/matplotlib/scripts/style_configurator.py | 20 | |
| LOW | skills/matplotlib/scripts/plot_template.py | 286 | |
| LOW | skills/venue-templates/scripts/validate_format.py | 15 | |
| LOW | skills/venue-templates/scripts/query_template.py | 14 | |
| LOW | skills/pytorch-lightning/scripts/quick_trainer_setup.py | 9 | |
| LOW | skills/pytorch-lightning/scripts/quick_trainer_setup.py | 9 | |
| LOW | …ills/clinical-reports/scripts/validate_trial_report.py | 14 | |
| 35 more matches not shown… | |||
| Severity | File | Line | Snippet |
|---|---|---|---|
| LOW | skills/pymc/scripts/model_comparison.py | 104 | # Check if difference is significant relative to SE |
| LOW | skills/research-lookup/scripts/generate_schematic_ai.py | 678 | # Check if quality is acceptable - STOP EARLY if so |
| LOW | …ls/get-available-resources/scripts/detect_resources.py | 156 | # Check if running on Apple Silicon |
| LOW | skills/iso-13485-certification/scripts/gap_analyzer.py | 207 | # Read file content (simple text reading) |
| LOW | skills/iso-13485-certification/scripts/gap_analyzer.py | 230 | # Check if any keyword appears in the document |
| LOW | …scientific-schematics/scripts/generate_schematic_ai.py | 678 | # Check if quality is acceptable - STOP EARLY if so |
| LOW | skills/deeptools/scripts/validate_files.py | 61 | # Check if start and end are integers |
| LOW | skills/deeptools/scripts/validate_files.py | 168 | # Check if any files were provided |
| LOW | skills/deeptools/scripts/validate_files.py | 180 | # Print results |
| LOW | skills/deeptools/scripts/workflow_generator.py | 417 | # Check if workflow was specified |
| LOW | skills/citation-management/scripts/extract_metadata.py | 46 | # Check if URL |
| LOW | …s/citation-management/scripts/generate_schematic_ai.py | 678 | # Check if quality is acceptable - STOP EARLY if so |
| LOW | skills/markitdown/scripts/generate_schematic_ai.py | 678 | # Check if quality is acceptable - STOP EARLY if so |
| LOW | skills/timesfm-forecasting/scripts/check_system.py | 388 | # Check if GPU is available |
| LOW | skills/infographics/scripts/generate_infographic_ai.py | 1142 | # Check if quality is acceptable |
| LOW | skills/pptx-posters/scripts/generate_schematic_ai.py | 678 | # Check if quality is acceptable - STOP EARLY if so |
| LOW | skills/treatment-plans/scripts/generate_schematic_ai.py | 678 | # Check if quality is acceptable - STOP EARLY if so |
| LOW | skills/treatment-plans/scripts/check_completeness.py | 295 | # Read file |
| LOW | skills/treatment-plans/scripts/check_completeness.py | 305 | # Display results |
| LOW | …lls/treatment-plans/scripts/validate_treatment_plan.py | 353 | # Display results |
| LOW | skills/treatment-plans/scripts/timeline_generator.py | 334 | # Check if any timeline info found |
| LOW | …ills/statistical-analysis/scripts/assumption_checks.py | 453 | # Check if grouped data |
| LOW | …ls/scientific-writing/scripts/generate_schematic_ai.py | 678 | # Check if quality is acceptable - STOP EARLY if so |
| LOW | …ical-decision-support/scripts/generate_schematic_ai.py | 678 | # Check if quality is acceptable - STOP EARLY if so |
| LOW | …ical-decision-support/scripts/validate_cds_document.py | 215 | # Check if gene appears but not in italics (\textit{} or \emph{}) |
| LOW | …nical-decision-support/scripts/create_cohort_tables.py | 47 | # Check if Fisher's exact is needed (expected count < 5) |
| LOW | skills/diffdock/scripts/analyze_results.py | 36 | # Check if this is a single complex or batch results |
| LOW | skills/diffdock/scripts/prepare_batch_csv.py | 130 | # Check if it's a file path or SMILES |
| LOW | skills/bioservices/scripts/protein_analysis_workflow.py | 76 | # Display results |
| LOW | …lls/literature-review/scripts/generate_schematic_ai.py | 678 | # Check if quality is acceptable - STOP EARLY if so |
| LOW | skills/literature-review/scripts/generate_pdf.py | 44 | # Check if pandoc is installed |
| LOW | …ls/scholar-evaluation/scripts/generate_schematic_ai.py | 678 | # Check if quality is acceptable - STOP EARLY if so |
| LOW | skills/deepchem/scripts/predict_solubility.py | 150 | # Display results |
| LOW | skills/latex-posters/scripts/generate_schematic_ai.py | 678 | # Check if quality is acceptable - STOP EARLY if so |
| LOW | skills/latex-posters/scripts/review_poster.sh | 13 | # Check if file argument provided |
| LOW | skills/latex-posters/scripts/review_poster.sh | 22 | # Check if file exists |
| LOW | skills/latex-posters/scripts/review_poster.sh | 93 | # Check if file is too large for email |
| LOW | skills/venue-templates/scripts/generate_schematic_ai.py | 678 | # Check if quality is acceptable - STOP EARLY if so |
| LOW | skills/venue-templates/scripts/validate_format.py | 175 | # Print results |
| LOW | …ills/clinical-reports/scripts/generate_schematic_ai.py | 678 | # Check if quality is acceptable - STOP EARLY if so |
| LOW | …lls/scientific-slides/scripts/validate_presentation.py | 387 | # Print results |
| LOW | …lls/scientific-slides/scripts/generate_schematic_ai.py | 678 | # Check if quality is acceptable - STOP EARLY if so |
| LOW | …hypothesis-generation/scripts/generate_schematic_ai.py | 678 | # Check if quality is acceptable - STOP EARLY if so |
| LOW | skills/rdkit/scripts/similarity_search.py | 288 | # Output results |
| LOW | skills/rdkit/scripts/molecular_properties.py | 131 | # Output results |
| LOW | skills/stable-baselines3/scripts/custom_env_template.py | 135 | # Check if goal is reached |
| LOW | skills/pufferlib/scripts/env_template.py | 102 | # Check if episode is done |
| LOW | skills/pymoo/scripts/many_objective_example.py | 44 | # Print results summary |
| LOW | skills/pymoo/scripts/single_objective_example.py | 45 | # Print results |
| LOW | skills/pymoo/scripts/multi_objective_example.py | 36 | # Print results summary |
| LOW | skills/labarchive-integration/scripts/setup_config.py | 167 | # Check if config already exists |
| LOW | skills/peer-review/scripts/generate_schematic_ai.py | 678 | # Check if quality is acceptable - STOP EARLY if so |
| Severity | File | Line | Snippet |
|---|---|---|---|
| MEDIUM | skills/research-lookup/research_lookup.py | 301 | return f"""You are an expert research assistant. Please provide comprehensive, accurate research information for |
| MEDIUM | skills/research-lookup/scripts/generate_schematic_ai.py | 74 | # Scientific diagram best practices prompt template |
| MEDIUM | skills/research-lookup/scripts/research_lookup.py | 301 | return f"""You are an expert research assistant. Please provide comprehensive, accurate research information for |
| MEDIUM | skills/iso-13485-certification/scripts/gap_analyzer.py | 249 | """Generate comprehensive gap analysis report.""" |
| MEDIUM | …scientific-schematics/scripts/generate_schematic_ai.py | 74 | # Scientific diagram best practices prompt template |
| MEDIUM | …s/citation-management/scripts/generate_schematic_ai.py | 74 | # Scientific diagram best practices prompt template |
| MEDIUM | skills/markitdown/scripts/generate_schematic_ai.py | 74 | # Scientific diagram best practices prompt template |
| MEDIUM | skills/pptx-posters/scripts/generate_schematic_ai.py | 74 | # Scientific diagram best practices prompt template |
| MEDIUM | skills/treatment-plans/scripts/generate_schematic_ai.py | 74 | # Scientific diagram best practices prompt template |
| MEDIUM | …lls/treatment-plans/scripts/validate_treatment_plan.py | 178 | """Display comprehensive validation results.""" |
| MEDIUM | …ills/statistical-analysis/scripts/assumption_checks.py | 186 | # Levene's test (robust to non-normality) |
| MEDIUM | …ills/statistical-analysis/scripts/assumption_checks.py | 533 | # Run comprehensive check |
| MEDIUM | …ls/scientific-writing/scripts/generate_schematic_ai.py | 74 | # Scientific diagram best practices prompt template |
| MEDIUM | …ical-decision-support/scripts/generate_schematic_ai.py | 74 | # Scientific diagram best practices prompt template |
| MEDIUM | …lls/literature-review/scripts/generate_schematic_ai.py | 74 | # Scientific diagram best practices prompt template |
| MEDIUM | …ls/scholar-evaluation/scripts/generate_schematic_ai.py | 74 | # Scientific diagram best practices prompt template |
| MEDIUM | skills/scholar-evaluation/scripts/calculate_scores.py | 149 | """Generate comprehensive evaluation report.""" |
| MEDIUM | …et-research-reports/scripts/generate_market_visuals.py | 15 | # Generate all 28 visuals (for comprehensive coverage) |
| MEDIUM | skills/latex-posters/scripts/generate_schematic_ai.py | 74 | # Scientific diagram best practices prompt template |
| MEDIUM | skills/matplotlib/scripts/plot_template.py | 317 | """Create a comprehensive figure with multiple subplots.""" |
| MEDIUM | skills/venue-templates/scripts/generate_schematic_ai.py | 74 | # Scientific diagram best practices prompt template |
| MEDIUM | …ills/clinical-reports/scripts/generate_schematic_ai.py | 74 | # Scientific diagram best practices prompt template |
| MEDIUM | skills/clinical-reports/scripts/validate_case_report.py | 192 | """Generate comprehensive validation report.""" |
| MEDIUM | …lls/scientific-slides/scripts/generate_schematic_ai.py | 74 | # Scientific diagram best practices prompt template |
| MEDIUM | …hypothesis-generation/scripts/generate_schematic_ai.py | 74 | # Scientific diagram best practices prompt template |
| MEDIUM | skills/rdkit/scripts/molecular_properties.py | 26 | """Calculate comprehensive molecular properties.""" |
| MEDIUM | skills/peer-review/scripts/generate_schematic_ai.py | 74 | # Scientific diagram best practices prompt template |
| Severity | File | Line | Snippet |
|---|---|---|---|
| LOW | skills/anndata/references/best_practices.md | 261 | ``` |
| LOW | skills/exploratory-data-analysis/SKILL.md | 301 | # 3. Analyze |
| LOW | skills/exploratory-data-analysis/SKILL.md | 321 | # 1. Detect: .nd2 → microscopy_imaging (Nikon format) |
| LOW | skills/bids/references/conversion_tools.md | 361 | #### Step 4: Convert |
| LOW | skills/bids/references/beps.yml | 1 | --- |
| LOW | skills/pymatgen/references/transformations_workflows.md | 301 | relax = MPRelaxSet(slab) |
| LOW | skills/markitdown/SKILL.md | 181 | Find plugins on GitHub with hashtag: `#markitdown-plugin` |
| LOW | skills/autoskill/config.yaml | 1 | # autoskill configuration |
| LOW | skills/autoskill/references/screenpipe-config.yaml | 1 | # Starter screenpipe configuration for autoskill users. |
| LOW | …forecasting/examples/global-temperature/run_example.sh | 1 | #!/bin/bash |
| LOW | …nical-decision-support/scripts/biomarker_classifier.py | 381 | # PT001,55.5,12.3,1+,Yes,14.2,1 |
| LOW | …inical-decision-support/scripts/build_decision_tree.py | 441 | # Example usage: |
| LOW | …nical-decision-support/scripts/create_cohort_tables.py | 521 | # PT001,Biomarker+,65,Male,0-1,IV,PR,1,0,... |
| LOW | skills/diffdock/assets/custom_inference_config.yaml | 41 | |
| LOW | skills/diffdock/assets/custom_inference_config.yaml | 61 | # temp_sampling_tor: 6.5 |
| LOW | skills/diffdock/assets/custom_inference_config.yaml | 81 | # temp_sampling_rot: 2.0 |
| LOW | skills/gget/references/workflows.md | 561 | # Step 5: Predict structures with AlphaFold (optional) |
| LOW | skills/literature-review/SKILL.md | 561 | --output search_results.md \ |
| LOW | …ls/literature-review/references/database_strategies.md | 421 | # 2. Search bioRxiv |
| LOW | skills/latex-posters/SKILL.md | 481 | python scripts/generate_schematic.py "POSTER FORMAT for A0. ONE case: Company logo + 'FDA APPROVED' (150pt bold) + '2024 |
| LOW | skills/pytorch-lightning/scripts/template_datamodule.py | 321 | print(f"Train batches: {len(train_loader)}") |
| LOW | skills/stable-baselines3/scripts/evaluate_agent.py | 201 | # Example 1: Evaluate a trained model |
| LOW | skills/stable-baselines3/scripts/evaluate_agent.py | 221 | # watch_agent( |
| LOW | skills/stable-baselines3/scripts/evaluate_agent.py | 241 | # model_path="./models/best_model/best_model.zip", |
| LOW | skills/stable-baselines3/scripts/train_rl_agent.py | 141 | algorithm=PPO, |
| LOW | skills/stable-baselines3/scripts/train_rl_agent.py | 161 | # algorithm=DQN, |
| LOW | skills/stable-baselines3/scripts/custom_env_template.py | 61 | # 2. Multi-discrete: spaces.MultiDiscrete([n1, n2, ...]) |
| LOW | skills/pufferlib/scripts/env_template.py | 41 | # 'position': (2,), |
| LOW | skills/optimize-for-gpu/SKILL.md | 261 | # For cudf.pandas accelerator mode, that's all you need |
| Severity | File | Line | Snippet |
|---|---|---|---|
| LOW | skills/pymc/scripts/model_comparison.py | 358 | # Example usage |
| LOW | skills/pymc/scripts/model_diagnostics.py | 328 | # Example usage |
| LOW | …forecasting/examples/global-temperature/run_example.sh | 9 | # Usage: |
| LOW | …ills/statistical-analysis/scripts/assumption_checks.py | 521 | # Example usage |
| LOW | …decision-support/scripts/generate_survival_analysis.py | 413 | # Example usage: |
| LOW | …ical-decision-support/scripts/validate_cds_document.py | 331 | # Example usage: |
| LOW | …nical-decision-support/scripts/biomarker_classifier.py | 375 | # Example usage: |
| LOW | …inical-decision-support/scripts/build_decision_tree.py | 441 | # Example usage: |
| LOW | …nical-decision-support/scripts/create_cohort_tables.py | 515 | # Example usage: |
| LOW | skills/simpy/scripts/resource_monitor.py | 320 | # Example usage |
| LOW | skills/pytorch-lightning/scripts/template_datamodule.py | 301 | # Example usage |
| LOW | …pytorch-lightning/scripts/template_lightning_module.py | 198 | # Example usage |
| LOW | …ills/scientific-visualization/scripts/figure_export.py | 318 | # Example usage |
| LOW | skills/scikit-learn/scripts/clustering_analysis.py | 338 | # Example usage |
| LOW | skills/scikit-learn/scripts/classification_pipeline.py | 230 | # Example usage |
| Severity | File | Line | Snippet |
|---|---|---|---|
| MEDIUM | skills/open-notebook/scripts/chat_interaction.py | 140 | # Create a notebook with some content first |
| MEDIUM | skills/open-notebook/scripts/chat_interaction.py | 162 | # Create a chat session |
| MEDIUM | skills/open-notebook/scripts/source_ingestion.py | 124 | # Create a notebook first |
| MEDIUM | skills/hypogenic/references/config_template.yaml | 116 | # Define a custom function in your code to parse specific output formats |
| MEDIUM | skills/pymoo/scripts/many_objective_example.py | 19 | # Define the problem - DTLZ2 with 5 objectives |
| MEDIUM | skills/pymoo/scripts/single_objective_example.py | 21 | # Define the problem - Sphere function (sum of squares) |
| MEDIUM | skills/pymoo/scripts/multi_objective_example.py | 18 | # Define the problem - ZDT1 (bi-objective) |
| Severity | File | Line | Snippet |
|---|---|---|---|
| HIGH | skills/latex-posters/SKILL.md | 114 | The #1 issue with AI-generated poster graphics is **TOO MUCH CONTENT**. This causes: |
| Severity | File | Line | Snippet |
|---|---|---|---|
| LOW | skills/pptx-posters/assets/poster_quality_checklist.md | 15 | - [ ] No placeholder text remaining (TODO, Lorem ipsum, etc.) |
| LOW | skills/latex-posters/SKILL.md | 1070 | - [ ] No placeholder text remaining (Lorem ipsum, TODO, etc.) |
| LOW | skills/latex-posters/scripts/review_poster.sh | 179 | echo " [ ] No placeholder text (Lorem ipsum, TODO, etc.)" |
| LOW | skills/latex-posters/assets/poster_quality_checklist.md | 15 | - [ ] No placeholder text remaining (TODO, Lorem ipsum, etc.) |