clearai-dsh 0.1.0

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  1. package/CHANGELOG.md +26 -0
  2. package/LICENSE +201 -0
  3. package/README.md +138 -0
  4. package/README.zh-CN.md +138 -0
  5. package/bin/clearai.mjs +224 -0
  6. package/brand/README.md +41 -0
  7. package/brand/logo-512-dark.png +0 -0
  8. package/brand/logo-512.png +0 -0
  9. package/brand/logo-lockup-dark.png +0 -0
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  11. package/brand/logo-lockup.svg +12 -0
  12. package/brand/logo-wordmark.svg +6 -0
  13. package/brand/logo.svg +19 -0
  14. package/cordis.patch.yml +39 -0
  15. package/lib/client.js +3071 -0
  16. package/lib/fold.js +1576 -0
  17. package/lib/host.js +605 -0
  18. package/package.json +65 -0
  19. package/presets/clearai/agent.cordis.yml +226 -0
  20. package/presets/clearai/plugins/brain.js +547 -0
  21. package/presets/clearai/plugins/clearai-kernel.js +5485 -0
  22. package/presets/clearai/plugins/ontology.js +306 -0
  23. package/presets/clearai/plugins/prompts.js +312 -0
  24. package/presets/clearai/preset.yml +5 -0
  25. package/presets/clearai/skills/clearai-loop/SKILL.md +89 -0
  26. package/presets/clearai/template/knowledge/README.md +25 -0
  27. package/presets/clearai/template/memory/README.md +34 -0
  28. package/presets/clearai/template/project.md +49 -0
  29. package/presets/clearai/template/skills/README.md +37 -0
  30. package/presets/clearai/template/skills/chart-diagram-qa/SKILL.md +43 -0
  31. package/presets/clearai/template/skills/citation-management/SKILL.md +73 -0
  32. package/presets/clearai/template/skills/citation-management/references/bibtex_formatting.md +908 -0
  33. package/presets/clearai/template/skills/citation-management/references/citation_validation.md +794 -0
  34. package/presets/clearai/template/skills/citation-management/references/google_scholar_search.md +725 -0
  35. package/presets/clearai/template/skills/citation-management/references/metadata_extraction.md +870 -0
  36. package/presets/clearai/template/skills/citation-management/references/pubmed_search.md +839 -0
  37. package/presets/clearai/template/skills/citation-management/scripts/doi_to_bibtex.py +204 -0
  38. package/presets/clearai/template/skills/citation-management/scripts/extract_metadata.py +569 -0
  39. package/presets/clearai/template/skills/citation-management/scripts/format_bibtex.py +349 -0
  40. package/presets/clearai/template/skills/citation-management/scripts/generate_schematic.py +139 -0
  41. package/presets/clearai/template/skills/citation-management/scripts/generate_schematic_ai.py +817 -0
  42. package/presets/clearai/template/skills/citation-management/scripts/search_google_scholar.py +282 -0
  43. package/presets/clearai/template/skills/citation-management/scripts/search_pubmed.py +398 -0
  44. package/presets/clearai/template/skills/citation-management/scripts/validate_citations.py +497 -0
  45. package/presets/clearai/template/skills/data-analysis/SKILL.md +92 -0
  46. package/presets/clearai/template/skills/data-analysis/checklists/readiness_check.md +23 -0
  47. package/presets/clearai/template/skills/data-analysis/templates/analysis_report.md.tpl +63 -0
  48. package/presets/clearai/template/skills/data-analysis/templates/cleaning_rules_draft.yaml.tpl +32 -0
  49. package/presets/clearai/template/skills/data-analysis/templates/data_dictionary.md.tpl +12 -0
  50. package/presets/clearai/template/skills/data-analysis/templates/domain_knowledge_template.md.tpl +316 -0
  51. package/presets/clearai/template/skills/data-analysis/templates/feature_candidates.json.tpl +20 -0
  52. package/presets/clearai/template/skills/data-analysis/templates/quality_scorecard.md.tpl +30 -0
  53. package/presets/clearai/template/skills/data-analysis/workflows/01-data-profiling.md +42 -0
  54. package/presets/clearai/template/skills/data-analysis/workflows/02-quality-audit.md +36 -0
  55. package/presets/clearai/template/skills/data-analysis/workflows/03-physical-correlation.md +25 -0
  56. package/presets/clearai/template/skills/data-analysis/workflows/04-unstructured-mining.md +26 -0
  57. package/presets/clearai/template/skills/data-qa-analysis/SKILL.md +102 -0
  58. package/presets/clearai/template/skills/data-qa-analysis/checklists/readiness_check.md +62 -0
  59. package/presets/clearai/template/skills/data-qa-analysis/templates/best_in_class_report.md.tpl +56 -0
  60. package/presets/clearai/template/skills/data-qa-analysis/templates/cleaning_rules_draft.yaml.tpl +56 -0
  61. package/presets/clearai/template/skills/data-qa-analysis/templates/data_dictionary.md.tpl +13 -0
  62. package/presets/clearai/template/skills/data-qa-analysis/templates/data_source_inventory_and_lineage.md.tpl +146 -0
  63. package/presets/clearai/template/skills/data-qa-analysis/templates/data_status_report.md.tpl +60 -0
  64. package/presets/clearai/template/skills/data-qa-analysis/templates/steady_state_rules.yaml.tpl +41 -0
  65. package/presets/clearai/template/skills/data-qa-analysis/templates/subsystem_registry.md.tpl +101 -0
  66. package/presets/clearai/template/skills/data-qa-analysis/templates/unified_execution_plan.md.tpl +100 -0
  67. package/presets/clearai/template/skills/data-qa-analysis/workflows/01-data-source-inventory-and-lineage.md +194 -0
  68. package/presets/clearai/template/skills/data-qa-analysis/workflows/02-data-alignment-and-tag-semantics.md +122 -0
  69. package/presets/clearai/template/skills/data-qa-analysis/workflows/03-steady-state-identification.md +126 -0
  70. package/presets/clearai/template/skills/data-qa-analysis/workflows/04-consumption-analysis.md +152 -0
  71. package/presets/clearai/template/skills/data-qa-analysis/workflows/05-best-in-class-and-optimization-space.md +78 -0
  72. package/presets/clearai/template/skills/domain-presearch/SKILL.md +131 -0
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  80. package/presets/clearai/template/skills/exploratory-data-analysis/references/general_scientific_formats.md +518 -0
  81. package/presets/clearai/template/skills/exploratory-data-analysis/references/microscopy_imaging_formats.md +620 -0
  82. package/presets/clearai/template/skills/exploratory-data-analysis/references/proteomics_metabolomics_formats.md +517 -0
  83. package/presets/clearai/template/skills/exploratory-data-analysis/references/spectroscopy_analytical_formats.md +633 -0
  84. package/presets/clearai/template/skills/exploratory-data-analysis/scripts/eda_analyzer.py +547 -0
  85. package/presets/clearai/template/skills/hypothesis-generation/SKILL.md +73 -0
  86. package/presets/clearai/template/skills/hypothesis-generation/references/experimental_design_patterns.md +329 -0
  87. package/presets/clearai/template/skills/hypothesis-generation/references/hypothesis_quality_criteria.md +198 -0
  88. package/presets/clearai/template/skills/hypothesis-generation/references/literature_search_strategies.md +622 -0
  89. package/presets/clearai/template/skills/hypothesis-generation/scripts/generate_schematic.py +139 -0
  90. package/presets/clearai/template/skills/hypothesis-generation/scripts/generate_schematic_ai.py +817 -0
  91. package/presets/clearai/template/skills/literature-review/SKILL.md +72 -0
  92. package/presets/clearai/template/skills/literature-review/references/citation_styles.md +166 -0
  93. package/presets/clearai/template/skills/literature-review/references/database_strategies.md +455 -0
  94. package/presets/clearai/template/skills/literature-review/scripts/generate_pdf.py +176 -0
  95. package/presets/clearai/template/skills/literature-review/scripts/generate_schematic.py +139 -0
  96. package/presets/clearai/template/skills/literature-review/scripts/generate_schematic_ai.py +817 -0
  97. package/presets/clearai/template/skills/literature-review/scripts/search_databases.py +303 -0
  98. package/presets/clearai/template/skills/literature-review/scripts/verify_citations.py +221 -0
  99. package/presets/clearai/template/skills/paper-lookup/SKILL.md +59 -0
  100. package/presets/clearai/template/skills/paper-lookup/references/arxiv.md +161 -0
  101. package/presets/clearai/template/skills/paper-lookup/references/biorxiv.md +118 -0
  102. package/presets/clearai/template/skills/paper-lookup/references/core.md +150 -0
  103. package/presets/clearai/template/skills/paper-lookup/references/crossref.md +181 -0
  104. package/presets/clearai/template/skills/paper-lookup/references/medrxiv.md +104 -0
  105. package/presets/clearai/template/skills/paper-lookup/references/openalex.md +174 -0
  106. package/presets/clearai/template/skills/paper-lookup/references/pmc.md +152 -0
  107. package/presets/clearai/template/skills/paper-lookup/references/pubmed.md +124 -0
  108. package/presets/clearai/template/skills/paper-lookup/references/semantic-scholar.md +203 -0
  109. package/presets/clearai/template/skills/paper-lookup/references/unpaywall.md +127 -0
  110. package/presets/clearai/template/skills/process-presearch/SKILL.md +196 -0
  111. package/presets/clearai/template/skills/process-presearch/checklists/process_checklist.md +18 -0
  112. package/presets/clearai/template/skills/process-presearch/references/figure_code.md +107 -0
  113. package/presets/clearai/template/skills/process-presearch/references/source_attribution_example.md +22 -0
  114. package/presets/clearai/template/skills/process-understanding-extraction/SKILL.md +69 -0
  115. package/presets/clearai/template/skills/process-understanding-extraction/checklists/readiness_check.md +34 -0
  116. package/presets/clearai/template/skills/process-understanding-extraction/templates/docx_raw_dump_extractor.py.tpl +132 -0
  117. package/presets/clearai/template/skills/process-understanding-extraction/templates/entity_map_unit_topology.json.tpl +86 -0
  118. package/presets/clearai/template/skills/process-understanding-extraction/templates/process_brief.md.tpl +89 -0
  119. package/presets/clearai/template/skills/process-understanding-extraction/templates/process_brief_builder_from_raw_dump.py.tpl +203 -0
  120. package/presets/clearai/template/skills/process-understanding-extraction/templates/process_flow_mermaid.md.tpl +41 -0
  121. package/presets/clearai/template/skills/process-understanding-extraction/templates/unified_execution_plan.md.tpl +53 -0
  122. package/presets/clearai/template/skills/process-understanding-extraction/workflows/01-process-doc-discovery.md +173 -0
  123. package/presets/clearai/template/skills/process-understanding-extraction/workflows/02-process-understanding-and-diagramming.md +106 -0
  124. package/presets/clearai/template/skills/scientific-brainstorming/SKILL.md +64 -0
  125. package/presets/clearai/template/skills/scientific-brainstorming/references/brainstorming_methods.md +326 -0
  126. package/presets/clearai/template/skills/scientific-critical-thinking/SKILL.md +72 -0
  127. package/presets/clearai/template/skills/scientific-critical-thinking/references/common_biases.md +364 -0
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  152. package/presets/clearai/template/skills/what-if-oracle/LICENSE.txt +5 -0
  153. package/presets/clearai/template/skills/what-if-oracle/SKILL.md +72 -0
  154. package/presets/clearai/template/skills/what-if-oracle/references/scenario-templates.md +154 -0
@@ -0,0 +1,139 @@
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+ #!/usr/bin/env python3
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+ """
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+ Scientific schematic generation using Nano Banana 2.
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+
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+ Generate any scientific diagram by describing it in natural language.
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+ Nano Banana 2 handles everything automatically with smart iterative refinement.
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+
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+ Smart iteration: Only regenerates if quality is below threshold for your document type.
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+ Quality review: Uses Gemini 3.1 Pro Preview for professional scientific evaluation.
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+
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+ Usage:
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+ # Generate for journal paper (highest quality threshold)
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+ python generate_schematic.py "CONSORT flowchart" -o flowchart.png --doc-type journal
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+
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+ # Generate for presentation (lower threshold, faster)
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+ python generate_schematic.py "Transformer architecture" -o transformer.png --doc-type presentation
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+
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+ # Generate for poster
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+ python generate_schematic.py "MAPK signaling pathway" -o pathway.png --doc-type poster
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+ """
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+
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+ import argparse
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+ import os
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+ import subprocess
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+ import sys
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+ from pathlib import Path
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+
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+
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+ def main():
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+ """Command-line interface."""
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+ parser = argparse.ArgumentParser(
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+ description="Generate scientific schematics using AI with smart iterative refinement",
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+ formatter_class=argparse.RawDescriptionHelpFormatter,
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+ epilog="""
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+ How it works:
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+ Simply describe your diagram in natural language
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+ Nano Banana 2 generates it automatically with:
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+ - Smart iteration (only regenerates if quality is below threshold)
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+ - Quality review by Gemini 3.1 Pro Preview
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+ - Document-type aware quality thresholds
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+ - Publication-ready output
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+
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+ Document Types (quality thresholds):
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+ journal 8.5/10 - Nature, Science, peer-reviewed journals
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+ conference 8.0/10 - Conference papers
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+ thesis 8.0/10 - Dissertations, theses
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+ grant 8.0/10 - Grant proposals
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+ preprint 7.5/10 - arXiv, bioRxiv, etc.
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+ report 7.5/10 - Technical reports
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+ poster 7.0/10 - Academic posters
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+ presentation 6.5/10 - Slides, talks
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+ default 7.5/10 - General purpose
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+
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+ Examples:
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+ # Generate for journal paper (strict quality)
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+ python generate_schematic.py "CONSORT participant flow" -o flowchart.png --doc-type journal
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+
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+ # Generate for poster (moderate quality)
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+ python generate_schematic.py "Transformer architecture" -o arch.png --doc-type poster
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+
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+ # Generate for slides (faster, lower threshold)
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+ python generate_schematic.py "System diagram" -o system.png --doc-type presentation
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+
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+ # Custom max iterations
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+ python generate_schematic.py "Complex pathway" -o pathway.png --iterations 2
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+
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+ # Verbose output
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+ python generate_schematic.py "Circuit diagram" -o circuit.png -v
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+
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+ Environment Variables:
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+ OPENROUTER_API_KEY Required for AI generation
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+ """
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+ )
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+
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+ parser.add_argument("prompt",
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+ help="Description of the diagram to generate")
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+ parser.add_argument("-o", "--output", required=True,
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+ help="Output file path")
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+ parser.add_argument("--doc-type", default="default",
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+ choices=["journal", "conference", "poster", "presentation",
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+ "report", "grant", "thesis", "preprint", "default"],
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+ help="Document type for quality threshold (default: default)")
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+ parser.add_argument("--iterations", type=int, default=2,
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+ help="Maximum refinement iterations (default: 2, max: 2)")
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+ parser.add_argument("--api-key",
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+ help="OpenRouter API key (or use OPENROUTER_API_KEY env var)")
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+ parser.add_argument("-v", "--verbose", action="store_true",
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+ help="Verbose output")
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+
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+ args = parser.parse_args()
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+
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+ # Check for API key
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+ api_key = args.api_key or os.getenv("OPENROUTER_API_KEY")
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+ if not api_key:
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+ print("Error: OPENROUTER_API_KEY environment variable not set")
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+ print("\nFor AI generation, you need an OpenRouter API key.")
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+ print("Get one at: https://openrouter.ai/keys")
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+ print("\nSet it with:")
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+ print(" export OPENROUTER_API_KEY='your_api_key'")
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+ print("\nOr use --api-key flag")
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+ sys.exit(1)
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+
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+ # Find AI generation script
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+ script_dir = Path(__file__).parent
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+ ai_script = script_dir / "generate_schematic_ai.py"
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+
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+ if not ai_script.exists():
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+ print(f"Error: AI generation script not found: {ai_script}")
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+ sys.exit(1)
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+
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+ # Build command
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+ cmd = [sys.executable, str(ai_script), args.prompt, "-o", args.output]
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+
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+ if args.doc_type != "default":
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+ cmd.extend(["--doc-type", args.doc_type])
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+
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+ # Enforce max 2 iterations
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+ iterations = min(args.iterations, 2)
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+ if iterations != 2:
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+ cmd.extend(["--iterations", str(iterations)])
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+
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+ if args.verbose:
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+ cmd.append("-v")
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+
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+ # Execute — pass API key via environment to avoid exposure in process listings
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+ try:
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+ env = os.environ.copy()
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+ if api_key:
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+ env["OPENROUTER_API_KEY"] = api_key
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+ result = subprocess.run(cmd, check=False, env=env)
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+ sys.exit(result.returncode)
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+ except Exception as e:
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+ print(f"Error executing AI generation: {e}")
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+ sys.exit(1)
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+
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+
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+ if __name__ == "__main__":
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+ main()
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+