@synsci/cli-darwin-x64 1.1.97 → 1.1.99

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (1549) hide show
  1. package/bin/synsc +0 -0
  2. package/package.json +1 -1
  3. package/bin/skills/accelerate/SKILL.md +0 -332
  4. package/bin/skills/accelerate/references/custom-plugins.md +0 -453
  5. package/bin/skills/accelerate/references/megatron-integration.md +0 -489
  6. package/bin/skills/accelerate/references/performance.md +0 -525
  7. package/bin/skills/adaptyv/SKILL.md +0 -114
  8. package/bin/skills/adaptyv/reference/api_reference.md +0 -308
  9. package/bin/skills/adaptyv/reference/examples.md +0 -913
  10. package/bin/skills/adaptyv/reference/experiments.md +0 -360
  11. package/bin/skills/adaptyv/reference/protein_optimization.md +0 -637
  12. package/bin/skills/aeon/SKILL.md +0 -374
  13. package/bin/skills/aeon/references/anomaly_detection.md +0 -154
  14. package/bin/skills/aeon/references/classification.md +0 -144
  15. package/bin/skills/aeon/references/clustering.md +0 -123
  16. package/bin/skills/aeon/references/datasets_benchmarking.md +0 -387
  17. package/bin/skills/aeon/references/distances.md +0 -256
  18. package/bin/skills/aeon/references/forecasting.md +0 -140
  19. package/bin/skills/aeon/references/networks.md +0 -289
  20. package/bin/skills/aeon/references/regression.md +0 -118
  21. package/bin/skills/aeon/references/segmentation.md +0 -163
  22. package/bin/skills/aeon/references/similarity_search.md +0 -187
  23. package/bin/skills/aeon/references/transformations.md +0 -246
  24. package/bin/skills/alphafold-database/SKILL.md +0 -513
  25. package/bin/skills/alphafold-database/references/api_reference.md +0 -423
  26. package/bin/skills/anndata/SKILL.md +0 -400
  27. package/bin/skills/anndata/references/best_practices.md +0 -525
  28. package/bin/skills/anndata/references/concatenation.md +0 -396
  29. package/bin/skills/anndata/references/data_structure.md +0 -314
  30. package/bin/skills/anndata/references/io_operations.md +0 -404
  31. package/bin/skills/anndata/references/manipulation.md +0 -516
  32. package/bin/skills/arboreto/SKILL.md +0 -243
  33. package/bin/skills/arboreto/references/algorithms.md +0 -138
  34. package/bin/skills/arboreto/references/basic_inference.md +0 -151
  35. package/bin/skills/arboreto/references/distributed_computing.md +0 -242
  36. package/bin/skills/arboreto/scripts/basic_grn_inference.py +0 -97
  37. package/bin/skills/astropy/SKILL.md +0 -331
  38. package/bin/skills/astropy/references/coordinates.md +0 -273
  39. package/bin/skills/astropy/references/cosmology.md +0 -307
  40. package/bin/skills/astropy/references/fits.md +0 -396
  41. package/bin/skills/astropy/references/tables.md +0 -489
  42. package/bin/skills/astropy/references/time.md +0 -404
  43. package/bin/skills/astropy/references/units.md +0 -178
  44. package/bin/skills/astropy/references/wcs_and_other_modules.md +0 -373
  45. package/bin/skills/audiocraft/SKILL.md +0 -564
  46. package/bin/skills/audiocraft/references/advanced-usage.md +0 -666
  47. package/bin/skills/audiocraft/references/troubleshooting.md +0 -504
  48. package/bin/skills/autogpt/SKILL.md +0 -403
  49. package/bin/skills/autogpt/references/advanced-usage.md +0 -535
  50. package/bin/skills/autogpt/references/troubleshooting.md +0 -420
  51. package/bin/skills/awq/SKILL.md +0 -310
  52. package/bin/skills/awq/references/advanced-usage.md +0 -324
  53. package/bin/skills/awq/references/troubleshooting.md +0 -344
  54. package/bin/skills/axolotl/SKILL.md +0 -158
  55. package/bin/skills/axolotl/references/api.md +0 -5548
  56. package/bin/skills/axolotl/references/dataset-formats.md +0 -1029
  57. package/bin/skills/axolotl/references/index.md +0 -15
  58. package/bin/skills/axolotl/references/other.md +0 -3563
  59. package/bin/skills/benchling-integration/SKILL.md +0 -480
  60. package/bin/skills/benchling-integration/references/api_endpoints.md +0 -883
  61. package/bin/skills/benchling-integration/references/authentication.md +0 -379
  62. package/bin/skills/benchling-integration/references/sdk_reference.md +0 -774
  63. package/bin/skills/bigcode-evaluation-harness/SKILL.md +0 -405
  64. package/bin/skills/bigcode-evaluation-harness/references/benchmarks.md +0 -393
  65. package/bin/skills/bigcode-evaluation-harness/references/custom-tasks.md +0 -424
  66. package/bin/skills/bigcode-evaluation-harness/references/issues.md +0 -394
  67. package/bin/skills/biopython/SKILL.md +0 -443
  68. package/bin/skills/biopython/references/advanced.md +0 -577
  69. package/bin/skills/biopython/references/alignment.md +0 -362
  70. package/bin/skills/biopython/references/blast.md +0 -455
  71. package/bin/skills/biopython/references/databases.md +0 -484
  72. package/bin/skills/biopython/references/phylogenetics.md +0 -566
  73. package/bin/skills/biopython/references/sequence_io.md +0 -285
  74. package/bin/skills/biopython/references/structure.md +0 -564
  75. package/bin/skills/biorxiv-database/SKILL.md +0 -483
  76. package/bin/skills/biorxiv-database/references/api_reference.md +0 -280
  77. package/bin/skills/biorxiv-database/scripts/biorxiv_search.py +0 -445
  78. package/bin/skills/bioservices/SKILL.md +0 -361
  79. package/bin/skills/bioservices/references/identifier_mapping.md +0 -685
  80. package/bin/skills/bioservices/references/services_reference.md +0 -636
  81. package/bin/skills/bioservices/references/workflow_patterns.md +0 -811
  82. package/bin/skills/bioservices/scripts/batch_id_converter.py +0 -347
  83. package/bin/skills/bioservices/scripts/compound_cross_reference.py +0 -378
  84. package/bin/skills/bioservices/scripts/pathway_analysis.py +0 -309
  85. package/bin/skills/bioservices/scripts/protein_analysis_workflow.py +0 -408
  86. package/bin/skills/bitsandbytes/SKILL.md +0 -411
  87. package/bin/skills/bitsandbytes/references/memory-optimization.md +0 -521
  88. package/bin/skills/bitsandbytes/references/qlora-training.md +0 -521
  89. package/bin/skills/bitsandbytes/references/quantization-formats.md +0 -447
  90. package/bin/skills/blip-2/SKILL.md +0 -564
  91. package/bin/skills/blip-2/references/advanced-usage.md +0 -680
  92. package/bin/skills/blip-2/references/troubleshooting.md +0 -526
  93. package/bin/skills/brenda-database/SKILL.md +0 -719
  94. package/bin/skills/brenda-database/references/api_reference.md +0 -537
  95. package/bin/skills/brenda-database/scripts/brenda_queries.py +0 -844
  96. package/bin/skills/brenda-database/scripts/brenda_visualization.py +0 -772
  97. package/bin/skills/brenda-database/scripts/enzyme_pathway_builder.py +0 -1053
  98. package/bin/skills/cellxgene-census/SKILL.md +0 -511
  99. package/bin/skills/cellxgene-census/references/census_schema.md +0 -182
  100. package/bin/skills/cellxgene-census/references/common_patterns.md +0 -351
  101. package/bin/skills/chembl-database/SKILL.md +0 -389
  102. package/bin/skills/chembl-database/references/api_reference.md +0 -272
  103. package/bin/skills/chembl-database/scripts/example_queries.py +0 -278
  104. package/bin/skills/chroma/SKILL.md +0 -406
  105. package/bin/skills/chroma/references/integration.md +0 -38
  106. package/bin/skills/cirq/SKILL.md +0 -346
  107. package/bin/skills/cirq/references/building.md +0 -307
  108. package/bin/skills/cirq/references/experiments.md +0 -572
  109. package/bin/skills/cirq/references/hardware.md +0 -515
  110. package/bin/skills/cirq/references/noise.md +0 -515
  111. package/bin/skills/cirq/references/simulation.md +0 -350
  112. package/bin/skills/cirq/references/transformation.md +0 -416
  113. package/bin/skills/citation-management/SKILL.md +0 -1109
  114. package/bin/skills/citation-management/assets/bibtex_template.bib +0 -264
  115. package/bin/skills/citation-management/assets/citation_checklist.md +0 -386
  116. package/bin/skills/citation-management/references/bibtex_formatting.md +0 -908
  117. package/bin/skills/citation-management/references/citation_validation.md +0 -794
  118. package/bin/skills/citation-management/references/google_scholar_search.md +0 -725
  119. package/bin/skills/citation-management/references/metadata_extraction.md +0 -870
  120. package/bin/skills/citation-management/references/pubmed_search.md +0 -839
  121. package/bin/skills/citation-management/scripts/doi_to_bibtex.py +0 -182
  122. package/bin/skills/citation-management/scripts/extract_metadata.py +0 -570
  123. package/bin/skills/citation-management/scripts/format_bibtex.py +0 -349
  124. package/bin/skills/citation-management/scripts/search_google_scholar.py +0 -251
  125. package/bin/skills/citation-management/scripts/search_pubmed.py +0 -348
  126. package/bin/skills/citation-management/scripts/validate_citations.py +0 -494
  127. package/bin/skills/clinical-decision-support/README.md +0 -129
  128. package/bin/skills/clinical-decision-support/SKILL.md +0 -506
  129. package/bin/skills/clinical-decision-support/assets/biomarker_report_template.tex +0 -380
  130. package/bin/skills/clinical-decision-support/assets/clinical_pathway_template.tex +0 -222
  131. package/bin/skills/clinical-decision-support/assets/cohort_analysis_template.tex +0 -359
  132. package/bin/skills/clinical-decision-support/assets/color_schemes.tex +0 -149
  133. package/bin/skills/clinical-decision-support/assets/example_gbm_cohort.md +0 -208
  134. package/bin/skills/clinical-decision-support/assets/recommendation_strength_guide.md +0 -328
  135. package/bin/skills/clinical-decision-support/assets/treatment_recommendation_template.tex +0 -529
  136. package/bin/skills/clinical-decision-support/references/biomarker_classification.md +0 -719
  137. package/bin/skills/clinical-decision-support/references/clinical_decision_algorithms.md +0 -604
  138. package/bin/skills/clinical-decision-support/references/evidence_synthesis.md +0 -840
  139. package/bin/skills/clinical-decision-support/references/outcome_analysis.md +0 -640
  140. package/bin/skills/clinical-decision-support/references/patient_cohort_analysis.md +0 -427
  141. package/bin/skills/clinical-decision-support/references/treatment_recommendations.md +0 -521
  142. package/bin/skills/clinical-decision-support/scripts/biomarker_classifier.py +0 -383
  143. package/bin/skills/clinical-decision-support/scripts/build_decision_tree.py +0 -417
  144. package/bin/skills/clinical-decision-support/scripts/create_cohort_tables.py +0 -509
  145. package/bin/skills/clinical-decision-support/scripts/generate_survival_analysis.py +0 -441
  146. package/bin/skills/clinical-decision-support/scripts/validate_cds_document.py +0 -326
  147. package/bin/skills/clinical-reports/IMPLEMENTATION_SUMMARY.md +0 -641
  148. package/bin/skills/clinical-reports/README.md +0 -236
  149. package/bin/skills/clinical-reports/SKILL.md +0 -1127
  150. package/bin/skills/clinical-reports/assets/case_report_template.md +0 -352
  151. package/bin/skills/clinical-reports/assets/clinical_trial_csr_template.md +0 -353
  152. package/bin/skills/clinical-reports/assets/clinical_trial_sae_template.md +0 -359
  153. package/bin/skills/clinical-reports/assets/consult_note_template.md +0 -305
  154. package/bin/skills/clinical-reports/assets/discharge_summary_template.md +0 -453
  155. package/bin/skills/clinical-reports/assets/hipaa_compliance_checklist.md +0 -395
  156. package/bin/skills/clinical-reports/assets/history_physical_template.md +0 -305
  157. package/bin/skills/clinical-reports/assets/lab_report_template.md +0 -309
  158. package/bin/skills/clinical-reports/assets/pathology_report_template.md +0 -249
  159. package/bin/skills/clinical-reports/assets/quality_checklist.md +0 -338
  160. package/bin/skills/clinical-reports/assets/radiology_report_template.md +0 -318
  161. package/bin/skills/clinical-reports/assets/soap_note_template.md +0 -253
  162. package/bin/skills/clinical-reports/references/case_report_guidelines.md +0 -570
  163. package/bin/skills/clinical-reports/references/clinical_trial_reporting.md +0 -693
  164. package/bin/skills/clinical-reports/references/data_presentation.md +0 -530
  165. package/bin/skills/clinical-reports/references/diagnostic_reports_standards.md +0 -629
  166. package/bin/skills/clinical-reports/references/medical_terminology.md +0 -588
  167. package/bin/skills/clinical-reports/references/patient_documentation.md +0 -744
  168. package/bin/skills/clinical-reports/references/peer_review_standards.md +0 -585
  169. package/bin/skills/clinical-reports/references/regulatory_compliance.md +0 -577
  170. package/bin/skills/clinical-reports/scripts/check_deidentification.py +0 -332
  171. package/bin/skills/clinical-reports/scripts/compliance_checker.py +0 -78
  172. package/bin/skills/clinical-reports/scripts/extract_clinical_data.py +0 -97
  173. package/bin/skills/clinical-reports/scripts/format_adverse_events.py +0 -97
  174. package/bin/skills/clinical-reports/scripts/generate_report_template.py +0 -149
  175. package/bin/skills/clinical-reports/scripts/terminology_validator.py +0 -126
  176. package/bin/skills/clinical-reports/scripts/validate_case_report.py +0 -323
  177. package/bin/skills/clinical-reports/scripts/validate_trial_report.py +0 -88
  178. package/bin/skills/clinicaltrials-database/SKILL.md +0 -507
  179. package/bin/skills/clinicaltrials-database/references/api_reference.md +0 -358
  180. package/bin/skills/clinicaltrials-database/scripts/query_clinicaltrials.py +0 -215
  181. package/bin/skills/clinpgx-database/SKILL.md +0 -638
  182. package/bin/skills/clinpgx-database/references/api_reference.md +0 -757
  183. package/bin/skills/clinpgx-database/scripts/query_clinpgx.py +0 -518
  184. package/bin/skills/clinvar-database/SKILL.md +0 -362
  185. package/bin/skills/clinvar-database/references/api_reference.md +0 -227
  186. package/bin/skills/clinvar-database/references/clinical_significance.md +0 -218
  187. package/bin/skills/clinvar-database/references/data_formats.md +0 -358
  188. package/bin/skills/clip/SKILL.md +0 -253
  189. package/bin/skills/clip/references/applications.md +0 -207
  190. package/bin/skills/cobrapy/SKILL.md +0 -463
  191. package/bin/skills/cobrapy/references/api_quick_reference.md +0 -655
  192. package/bin/skills/cobrapy/references/workflows.md +0 -593
  193. package/bin/skills/colab-finetuning/SKILL.md +0 -153
  194. package/bin/skills/colab-finetuning/references/bridge-setup.md +0 -68
  195. package/bin/skills/colab-finetuning/references/gpu-tiers.md +0 -54
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  197. package/bin/skills/constitutional-ai/SKILL.md +0 -290
  198. package/bin/skills/cosmic-database/SKILL.md +0 -336
  199. package/bin/skills/cosmic-database/references/cosmic_data_reference.md +0 -220
  200. package/bin/skills/cosmic-database/scripts/download_cosmic.py +0 -231
  201. package/bin/skills/crewai/SKILL.md +0 -498
  202. package/bin/skills/crewai/references/flows.md +0 -438
  203. package/bin/skills/crewai/references/tools.md +0 -429
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  205. package/bin/skills/dask/SKILL.md +0 -456
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  209. package/bin/skills/dask/references/dataframes.md +0 -368
  210. package/bin/skills/dask/references/futures.md +0 -541
  211. package/bin/skills/dask/references/schedulers.md +0 -504
  212. package/bin/skills/datacommons-client/SKILL.md +0 -255
  213. package/bin/skills/datacommons-client/references/getting_started.md +0 -417
  214. package/bin/skills/datacommons-client/references/node.md +0 -250
  215. package/bin/skills/datacommons-client/references/observation.md +0 -185
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  217. package/bin/skills/datamol/SKILL.md +0 -706
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  224. package/bin/skills/deepchem/SKILL.md +0 -597
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  227. package/bin/skills/deepchem/scripts/graph_neural_network.py +0 -338
  228. package/bin/skills/deepchem/scripts/predict_solubility.py +0 -224
  229. package/bin/skills/deepchem/scripts/transfer_learning.py +0 -375
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@@ -1,837 +0,0 @@
1
- #!/usr/bin/env python3
2
- """
3
- AI-powered scientific schematic generation using Nano Banana Pro.
4
-
5
- This script uses a smart iterative refinement approach:
6
- 1. Generate initial image with Nano Banana Pro
7
- 2. AI quality review using Gemini 3 Pro for scientific critique
8
- 3. Only regenerate if quality is below threshold for document type
9
- 4. Repeat until quality meets standards (max iterations)
10
-
11
- Requirements:
12
- - OPENROUTER_API_KEY environment variable
13
- - requests library
14
-
15
- Usage:
16
- python generate_schematic_ai.py "Create a flowchart showing CONSORT participant flow" -o flowchart.png
17
- python generate_schematic_ai.py "Neural network architecture diagram" -o architecture.png --iterations 2
18
- python generate_schematic_ai.py "Simple block diagram" -o diagram.png --doc-type poster
19
- """
20
-
21
- import argparse
22
- import base64
23
- import json
24
- import os
25
- import sys
26
- import time
27
- from pathlib import Path
28
- from typing import Any, Dict, List, Optional, Tuple
29
-
30
-
31
- try:
32
- import requests
33
- except ImportError:
34
- print("Error: requests library not found. Install with: pip install requests")
35
- sys.exit(1)
36
-
37
-
38
- # Try to load .env file from multiple potential locations
39
- def _load_env_file():
40
- """Load .env file from current directory, parent directories, or package directory.
41
-
42
- Returns True if a .env file was found and loaded, False otherwise.
43
- Note: This does NOT override existing environment variables.
44
- """
45
- try:
46
- from dotenv import load_dotenv
47
- except ImportError:
48
- return False # python-dotenv not installed
49
-
50
- # Try current working directory first
51
- env_path = Path.cwd() / ".env"
52
- if env_path.exists():
53
- load_dotenv(dotenv_path=env_path, override=False)
54
- return True
55
-
56
- # Try parent directories (up to 5 levels)
57
- cwd = Path.cwd()
58
- for _ in range(5):
59
- env_path = cwd / ".env"
60
- if env_path.exists():
61
- load_dotenv(dotenv_path=env_path, override=False)
62
- return True
63
- cwd = cwd.parent
64
- if cwd == cwd.parent: # Reached root
65
- break
66
-
67
- # Try the package's parent directory (scientific-writer project root)
68
- script_dir = Path(__file__).resolve().parent
69
- for _ in range(5):
70
- env_path = script_dir / ".env"
71
- if env_path.exists():
72
- load_dotenv(dotenv_path=env_path, override=False)
73
- return True
74
- script_dir = script_dir.parent
75
- if script_dir == script_dir.parent:
76
- break
77
-
78
- return False
79
-
80
-
81
- class ScientificSchematicGenerator:
82
- """Generate scientific schematics using AI with smart iterative refinement.
83
-
84
- Uses Nano Banana Pro (with Nano Banana Standard fallback) for generation
85
- and Gemini 3.1 Pro for quality review. Multiple passes only occur if the
86
- generated schematic doesn't meet the quality threshold for the target
87
- document type.
88
- """
89
-
90
- # Quality thresholds by document type (score out of 10)
91
- # Higher thresholds for more formal publications
92
- QUALITY_THRESHOLDS = {
93
- "journal": 8.5, # Nature, Science, etc. - highest standards
94
- "conference": 8.0, # Conference papers - high standards
95
- "poster": 7.0, # Academic posters - good quality
96
- "presentation": 6.5, # Slides/talks - clear but less formal
97
- "report": 7.5, # Technical reports - professional
98
- "grant": 8.0, # Grant proposals - must be compelling
99
- "thesis": 8.0, # Dissertations - formal academic
100
- "preprint": 7.5, # arXiv, etc. - good quality
101
- "default": 7.5, # Default threshold
102
- }
103
-
104
- # Scientific diagram best practices prompt template
105
- SCIENTIFIC_DIAGRAM_GUIDELINES = """
106
- Create a high-quality scientific diagram with these requirements:
107
-
108
- VISUAL QUALITY:
109
- - Clean white or light background (no textures or gradients)
110
- - High contrast for readability and printing
111
- - Professional, publication-ready appearance
112
- - Sharp, clear lines and text
113
- - Adequate spacing between elements to prevent crowding
114
-
115
- TYPOGRAPHY:
116
- - Clear, readable sans-serif fonts (Arial, Helvetica style)
117
- - Minimum 10pt font size for all labels
118
- - Consistent font sizes throughout
119
- - All text horizontal or clearly readable
120
- - No overlapping text
121
-
122
- SCIENTIFIC STANDARDS:
123
- - Accurate representation of concepts
124
- - Clear labels for all components
125
- - Include scale bars, legends, or axes where appropriate
126
- - Use standard scientific notation and symbols
127
- - Include units where applicable
128
-
129
- ACCESSIBILITY:
130
- - Colorblind-friendly color palette (use Okabe-Ito colors if using color)
131
- - High contrast between elements
132
- - Redundant encoding (shapes + colors, not just colors)
133
- - Works well in grayscale
134
-
135
- LAYOUT:
136
- - Logical flow (left-to-right or top-to-bottom)
137
- - Clear visual hierarchy
138
- - Balanced composition
139
- - Appropriate use of whitespace
140
- - No clutter or unnecessary decorative elements
141
- """
142
-
143
- def __init__(self, api_key: Optional[str] = None, verbose: bool = False):
144
- """
145
- Initialize the generator.
146
-
147
- Args:
148
- api_key: OpenRouter API key (or use OPENROUTER_API_KEY env var)
149
- verbose: Print detailed progress information
150
- """
151
- # Priority: 1) explicit api_key param, 2) environment variable, 3) .env file
152
- self.api_key = api_key or os.getenv("OPENROUTER_API_KEY")
153
-
154
- # If not found in environment, try loading from .env file
155
- if not self.api_key:
156
- _load_env_file()
157
- self.api_key = os.getenv("OPENROUTER_API_KEY")
158
-
159
- if not self.api_key:
160
- raise ValueError(
161
- "OPENROUTER_API_KEY not found. Please either:\n"
162
- " 1. Set the OPENROUTER_API_KEY environment variable\n"
163
- " 2. Add OPENROUTER_API_KEY to your .env file\n"
164
- " 3. Pass api_key parameter to the constructor\n"
165
- "Get your API key from: https://openrouter.ai/keys"
166
- )
167
-
168
- self.verbose = verbose
169
- self._last_error = None # Track last error for better reporting
170
- self.base_url = "https://openrouter.ai/api/v1"
171
- # Image generation models in priority order (fallback if primary fails)
172
- # Nano Banana Pro - Google's advanced image generation model
173
- self.image_models = [
174
- "google/gemini-3-pro-image-preview", # Nano Banana Pro (best quality)
175
- "google/gemini-2.5-flash-image", # Nano Banana Standard (fallback)
176
- ]
177
- self.image_model = self.image_models[0]
178
- # Gemini 3.1 Pro for quality review - excellent vision and reasoning
179
- self.review_model = "google/gemini-3.1-pro-preview"
180
-
181
- def _log(self, message: str):
182
- """Log message if verbose mode is enabled."""
183
- if self.verbose:
184
- print(f"[{time.strftime('%H:%M:%S')}] {message}")
185
-
186
- def _make_request(
187
- self, model: str, messages: List[Dict[str, Any]], modalities: Optional[List[str]] = None
188
- ) -> Dict[str, Any]:
189
- """
190
- Make a request to OpenRouter API.
191
-
192
- Args:
193
- model: Model identifier
194
- messages: List of message dictionaries
195
- modalities: Optional list of modalities (e.g., ["image", "text"])
196
-
197
- Returns:
198
- API response as dictionary
199
- """
200
- headers = {
201
- "Authorization": f"Bearer {self.api_key}",
202
- "Content-Type": "application/json",
203
- "HTTP-Referer": "https://github.com/scientific-writer",
204
- "X-Title": "Scientific Schematic Generator",
205
- }
206
-
207
- payload = {"model": model, "messages": messages}
208
-
209
- if modalities:
210
- payload["modalities"] = modalities
211
-
212
- self._log(f"Making request to {model}...")
213
-
214
- try:
215
- response = requests.post(f"{self.base_url}/chat/completions", headers=headers, json=payload, timeout=120)
216
-
217
- # Try to get response body even on error
218
- try:
219
- response_json = response.json()
220
- except json.JSONDecodeError:
221
- response_json = {"raw_text": response.text[:500]}
222
-
223
- # Check for HTTP errors but include response body in error message
224
- if response.status_code != 200:
225
- error_detail = response_json.get("error", response_json)
226
- self._log(f"HTTP {response.status_code}: {error_detail}")
227
- raise RuntimeError(f"API request failed (HTTP {response.status_code}): {error_detail}")
228
-
229
- return response_json
230
- except requests.exceptions.Timeout:
231
- raise RuntimeError("API request timed out after 120 seconds")
232
- except requests.exceptions.RequestException as e:
233
- raise RuntimeError(f"API request failed: {str(e)}")
234
-
235
- def _extract_image_from_response(self, response: Dict[str, Any]) -> Optional[bytes]:
236
- """
237
- Extract base64-encoded image from API response.
238
-
239
- For Nano Banana Pro, images are returned in the 'images' field of the message,
240
- not in the 'content' field.
241
-
242
- Args:
243
- response: API response dictionary
244
-
245
- Returns:
246
- Image bytes or None if not found
247
- """
248
- try:
249
- choices = response.get("choices", [])
250
- if not choices:
251
- self._log("No choices in response")
252
- return None
253
-
254
- message = choices[0].get("message", {})
255
-
256
- # IMPORTANT: Nano Banana Pro returns images in the 'images' field
257
- images = message.get("images", [])
258
- if images and len(images) > 0:
259
- self._log(f"Found {len(images)} image(s) in 'images' field")
260
-
261
- # Get first image
262
- first_image = images[0]
263
- if isinstance(first_image, dict):
264
- # Extract image_url
265
- if first_image.get("type") == "image_url":
266
- url = first_image.get("image_url", {})
267
- if isinstance(url, dict):
268
- url = url.get("url", "")
269
-
270
- if url and url.startswith("data:image"):
271
- # Extract base64 data after comma
272
- if "," in url:
273
- base64_str = url.split(",", 1)[1]
274
- # Clean whitespace
275
- base64_str = base64_str.replace('\n', '').replace('\r', '').replace(' ', '')
276
- self._log(f"Extracted base64 data (length: {len(base64_str)})")
277
- return base64.b64decode(base64_str)
278
-
279
- # Fallback: check content field (for other models or future changes)
280
- content = message.get("content", "")
281
-
282
- if self.verbose:
283
- self._log(f"Content type: {type(content)}, length: {len(str(content))}")
284
-
285
- # Handle string content
286
- if isinstance(content, str) and "data:image" in content:
287
- import re
288
-
289
- match = re.search(r'data:image/[^;]+;base64,([A-Za-z0-9+/=\n\r]+)', content, re.DOTALL)
290
- if match:
291
- base64_str = match.group(1).replace('\n', '').replace('\r', '').replace(' ', '')
292
- self._log(f"Found image in content field (length: {len(base64_str)})")
293
- return base64.b64decode(base64_str)
294
-
295
- # Handle list content
296
- if isinstance(content, list):
297
- for i, block in enumerate(content):
298
- if isinstance(block, dict) and block.get("type") == "image_url":
299
- url = block.get("image_url", {})
300
- if isinstance(url, dict):
301
- url = url.get("url", "")
302
- if url and url.startswith("data:image") and "," in url:
303
- base64_str = url.split(",", 1)[1].replace('\n', '').replace('\r', '').replace(' ', '')
304
- self._log(f"Found image in content block {i}")
305
- return base64.b64decode(base64_str)
306
-
307
- self._log("No image data found in response")
308
- return None
309
-
310
- except Exception as e:
311
- self._log(f"Error extracting image: {str(e)}")
312
- import traceback
313
-
314
- if self.verbose:
315
- traceback.print_exc()
316
- return None
317
-
318
- def _image_to_base64(self, image_path: str) -> str:
319
- """
320
- Convert image file to base64 data URL.
321
-
322
- Args:
323
- image_path: Path to image file
324
-
325
- Returns:
326
- Base64 data URL string
327
- """
328
- with open(image_path, "rb") as f:
329
- image_data = f.read()
330
-
331
- # Determine image type from extension
332
- ext = Path(image_path).suffix.lower()
333
- mime_type = {
334
- ".png": "image/png",
335
- ".jpg": "image/jpeg",
336
- ".jpeg": "image/jpeg",
337
- ".gif": "image/gif",
338
- ".webp": "image/webp",
339
- }.get(ext, "image/png")
340
-
341
- base64_data = base64.b64encode(image_data).decode("utf-8")
342
- return f"data:{mime_type};base64,{base64_data}"
343
-
344
- def _diagnose_response(self, response: Dict[str, Any], model: str):
345
- """Print diagnostic info when image extraction fails."""
346
- print(f" [diagnostic] Model: {model}")
347
- if "error" in response:
348
- print(f" [diagnostic] API error: {response['error']}")
349
- if "choices" in response and response["choices"]:
350
- msg = response["choices"][0].get("message", {})
351
- print(f" [diagnostic] Message keys: {list(msg.keys())}")
352
- finish = response["choices"][0].get("finish_reason", "unknown")
353
- print(f" [diagnostic] Finish reason: {finish}")
354
- content = msg.get("content", "")
355
- if isinstance(content, str):
356
- preview = content[:300] + "..." if len(content) > 300 else content
357
- if preview:
358
- print(f" [diagnostic] Content: {preview}")
359
- elif isinstance(content, list):
360
- print(f" [diagnostic] Content is list with {len(content)} items:")
361
- for i, item in enumerate(content[:5]):
362
- if isinstance(item, dict):
363
- print(f" Item {i}: type={item.get('type')}, keys={list(item.keys())}")
364
- images = msg.get("images", [])
365
- if images:
366
- print(f" [diagnostic] Images field: {len(images)} items")
367
- reasoning = msg.get("reasoning", "")
368
- if reasoning:
369
- preview = reasoning[:200] + "..." if len(reasoning) > 200 else reasoning
370
- print(f" [diagnostic] Reasoning: {preview}")
371
- else:
372
- print(f" [diagnostic] Response keys: {list(response.keys())}")
373
- # Show raw response preview (truncated)
374
- raw = json.dumps(response)[:500]
375
- print(f" [diagnostic] Raw response: {raw}")
376
-
377
- def _try_generate_with_model(self, model: str, messages: List[Dict[str, Any]]) -> Optional[bytes]:
378
- """Try to generate an image with a specific model. Returns image bytes or None."""
379
- try:
380
- response = self._make_request(model=model, messages=messages, modalities=["image", "text"])
381
-
382
- # Check for API errors in response body
383
- if "error" in response:
384
- error_msg = response["error"]
385
- if isinstance(error_msg, dict):
386
- error_msg = error_msg.get("message", str(error_msg))
387
- print(f" ✗ {model}: API error — {error_msg}")
388
- return None
389
-
390
- image_data = self._extract_image_from_response(response)
391
- if image_data:
392
- self._log(f"✓ Generated image with {model} ({len(image_data)} bytes)")
393
- return image_data
394
-
395
- # Image extraction failed — print diagnostics
396
- print(f" ✗ {model}: No image data in response")
397
- self._diagnose_response(response, model)
398
- return None
399
-
400
- except RuntimeError as e:
401
- print(f" ✗ {model}: {str(e)}")
402
- return None
403
- except Exception as e:
404
- print(f" ✗ {model}: Unexpected error — {str(e)}")
405
- if self.verbose:
406
- import traceback
407
- traceback.print_exc()
408
- return None
409
-
410
- def generate_image(self, prompt: str) -> Optional[bytes]:
411
- """
412
- Generate an image using available image models with automatic fallback.
413
-
414
- Tries each model in priority order. If the primary model fails or returns
415
- no image data, falls back to the next model.
416
-
417
- Args:
418
- prompt: Description of the diagram to generate
419
-
420
- Returns:
421
- Image bytes or None if all models failed
422
- """
423
- self._last_error = None
424
-
425
- messages = [{"role": "user", "content": prompt}]
426
-
427
- for model in self.image_models:
428
- self._log(f"Trying {model}...")
429
- image_data = self._try_generate_with_model(model, messages)
430
- if image_data:
431
- self.image_model = model # Track which model succeeded
432
- return image_data
433
-
434
- self._last_error = f"All image models failed: {', '.join(self.image_models)}"
435
- return None
436
-
437
- def review_image(
438
- self, image_path: str, original_prompt: str, iteration: int, doc_type: str = "default", max_iterations: int = 2
439
- ) -> Tuple[str, float, bool]:
440
- """
441
- Review generated image using Gemini 3 Pro for quality analysis.
442
-
443
- Uses Gemini 3 Pro's superior vision and reasoning capabilities to
444
- evaluate the schematic quality and determine if regeneration is needed.
445
-
446
- Args:
447
- image_path: Path to the generated image
448
- original_prompt: Original user prompt
449
- iteration: Current iteration number
450
- doc_type: Document type (journal, poster, presentation, etc.)
451
- max_iterations: Maximum iterations allowed
452
-
453
- Returns:
454
- Tuple of (critique text, quality score 0-10, needs_improvement bool)
455
- """
456
- # Use Gemini 3 Pro for review - excellent vision and analysis
457
- image_data_url = self._image_to_base64(image_path)
458
-
459
- # Get quality threshold for this document type
460
- threshold = self.QUALITY_THRESHOLDS.get(doc_type.lower(), self.QUALITY_THRESHOLDS["default"])
461
-
462
- review_prompt = f"""You are an expert reviewer evaluating a scientific diagram for publication quality.
463
-
464
- ORIGINAL REQUEST: {original_prompt}
465
-
466
- DOCUMENT TYPE: {doc_type} (quality threshold: {threshold}/10)
467
- ITERATION: {iteration}/{max_iterations}
468
-
469
- Carefully evaluate this diagram on these criteria:
470
-
471
- 1. **Scientific Accuracy** (0-2 points)
472
- - Correct representation of concepts
473
- - Proper notation and symbols
474
- - Accurate relationships shown
475
-
476
- 2. **Clarity and Readability** (0-2 points)
477
- - Easy to understand at a glance
478
- - Clear visual hierarchy
479
- - No ambiguous elements
480
-
481
- 3. **Label Quality** (0-2 points)
482
- - All important elements labeled
483
- - Labels are readable (appropriate font size)
484
- - Consistent labeling style
485
-
486
- 4. **Layout and Composition** (0-2 points)
487
- - Logical flow (top-to-bottom or left-to-right)
488
- - Balanced use of space
489
- - No overlapping elements
490
-
491
- 5. **Professional Appearance** (0-2 points)
492
- - Publication-ready quality
493
- - Clean, crisp lines and shapes
494
- - Appropriate colors/contrast
495
-
496
- RESPOND IN THIS EXACT FORMAT:
497
- SCORE: [total score 0-10]
498
-
499
- STRENGTHS:
500
- - [strength 1]
501
- - [strength 2]
502
-
503
- ISSUES:
504
- - [issue 1 if any]
505
- - [issue 2 if any]
506
-
507
- VERDICT: [ACCEPTABLE or NEEDS_IMPROVEMENT]
508
-
509
- If score >= {threshold}, the diagram is ACCEPTABLE for {doc_type} publication.
510
- If score < {threshold}, mark as NEEDS_IMPROVEMENT with specific suggestions."""
511
-
512
- messages = [
513
- {
514
- "role": "user",
515
- "content": [
516
- {"type": "text", "text": review_prompt},
517
- {"type": "image_url", "image_url": {"url": image_data_url}},
518
- ],
519
- }
520
- ]
521
-
522
- try:
523
- # Use Gemini 3 Pro for high-quality review
524
- response = self._make_request(model=self.review_model, messages=messages)
525
-
526
- # Extract text response
527
- choices = response.get("choices", [])
528
- if not choices:
529
- return "Image generated successfully", 8.0
530
-
531
- message = choices[0].get("message", {})
532
- content = message.get("content", "")
533
-
534
- # Check reasoning field (Nano Banana Pro puts analysis here)
535
- reasoning = message.get("reasoning", "")
536
- if reasoning and not content:
537
- content = reasoning
538
-
539
- if isinstance(content, list):
540
- # Extract text from content blocks
541
- text_parts = []
542
- for block in content:
543
- if isinstance(block, dict) and block.get("type") == "text":
544
- text_parts.append(block.get("text", ""))
545
- content = "\n".join(text_parts)
546
-
547
- # Try to extract score
548
- score = 7.5 # Default score if extraction fails
549
- import re
550
-
551
- # Look for SCORE: X or SCORE: X/10 format
552
- score_match = re.search(r'SCORE:\s*(\d+(?:\.\d+)?)', content, re.IGNORECASE)
553
- if score_match:
554
- score = float(score_match.group(1))
555
- else:
556
- # Fallback: look for any score pattern
557
- score_match = re.search(
558
- r'(?:score|rating|quality)[:\s]+(\d+(?:\.\d+)?)\s*(?:/\s*10)?', content, re.IGNORECASE
559
- )
560
- if score_match:
561
- score = float(score_match.group(1))
562
-
563
- # Determine if improvement is needed based on verdict or score
564
- needs_improvement = False
565
- if "NEEDS_IMPROVEMENT" in content.upper():
566
- needs_improvement = True
567
- elif score < threshold:
568
- needs_improvement = True
569
-
570
- self._log(f"✓ Review complete (Score: {score}/10, Threshold: {threshold}/10)")
571
- self._log(f" Verdict: {'Needs improvement' if needs_improvement else 'Acceptable'}")
572
-
573
- return (content if content else "Image generated successfully", score, needs_improvement)
574
- except Exception as e:
575
- self._log(f"Review skipped: {str(e)}")
576
- # Don't fail the whole process if review fails - assume acceptable
577
- return "Image generated successfully (review skipped)", 7.5, False
578
-
579
- def improve_prompt(self, original_prompt: str, critique: str, iteration: int) -> str:
580
- """
581
- Improve the generation prompt based on critique.
582
-
583
- Args:
584
- original_prompt: Original user prompt
585
- critique: Review critique from previous iteration
586
- iteration: Current iteration number
587
-
588
- Returns:
589
- Improved prompt for next generation
590
- """
591
- improved_prompt = f"""{self.SCIENTIFIC_DIAGRAM_GUIDELINES}
592
-
593
- USER REQUEST: {original_prompt}
594
-
595
- ITERATION {iteration}: Based on previous feedback, address these specific improvements:
596
- {critique}
597
-
598
- Generate an improved version that addresses all the critique points while maintaining scientific accuracy and professional quality."""
599
-
600
- return improved_prompt
601
-
602
- def generate_iterative(
603
- self, user_prompt: str, output_path: str, iterations: int = 2, doc_type: str = "default"
604
- ) -> Dict[str, Any]:
605
- """
606
- Generate scientific schematic with smart iterative refinement.
607
-
608
- Only regenerates if the quality score is below the threshold for the
609
- specified document type. This saves API calls and time when the first
610
- generation is already good enough.
611
-
612
- Args:
613
- user_prompt: User's description of desired diagram
614
- output_path: Path to save final image
615
- iterations: Maximum refinement iterations (default: 2, max: 2)
616
- doc_type: Document type for quality threshold (journal, poster, etc.)
617
-
618
- Returns:
619
- Dictionary with generation results and metadata
620
- """
621
- output_path = Path(output_path)
622
- output_dir = output_path.parent
623
- output_dir.mkdir(parents=True, exist_ok=True)
624
-
625
- base_name = output_path.stem
626
- extension = output_path.suffix or ".png"
627
-
628
- # Get quality threshold for this document type
629
- threshold = self.QUALITY_THRESHOLDS.get(doc_type.lower(), self.QUALITY_THRESHOLDS["default"])
630
-
631
- results = {
632
- "user_prompt": user_prompt,
633
- "doc_type": doc_type,
634
- "quality_threshold": threshold,
635
- "iterations": [],
636
- "final_image": None,
637
- "final_score": 0.0,
638
- "success": False,
639
- "early_stop": False,
640
- "early_stop_reason": None,
641
- }
642
-
643
- current_prompt = f"""{self.SCIENTIFIC_DIAGRAM_GUIDELINES}
644
-
645
- USER REQUEST: {user_prompt}
646
-
647
- Generate a publication-quality scientific diagram that meets all the guidelines above."""
648
-
649
- print(f"\n{'=' * 60}")
650
- print("Generating Scientific Schematic")
651
- print(f"{'=' * 60}")
652
- print(f"Description: {user_prompt}")
653
- print(f"Document Type: {doc_type}")
654
- print(f"Quality Threshold: {threshold}/10")
655
- print(f"Max Iterations: {iterations}")
656
- print(f"Image Models: {' → '.join(self.image_models)}")
657
- print(f"Review Model: {self.review_model}")
658
- print(f"Output: {output_path}")
659
- print(f"{'=' * 60}\n")
660
-
661
- for i in range(1, iterations + 1):
662
- print(f"\n[Iteration {i}/{iterations}]")
663
- print("-" * 40)
664
-
665
- # Generate image
666
- print("Generating image...")
667
- image_data = self.generate_image(current_prompt)
668
-
669
- if not image_data:
670
- error_msg = getattr(self, '_last_error', 'Image generation failed - no image data returned')
671
- print(f"✗ Generation failed: {error_msg}")
672
- results["iterations"].append({"iteration": i, "success": False, "error": error_msg})
673
- continue
674
-
675
- # Save iteration image
676
- iter_path = output_dir / f"{base_name}_v{i}{extension}"
677
- with open(iter_path, "wb") as f:
678
- f.write(image_data)
679
- print(f"✓ Saved: {iter_path}")
680
-
681
- # Review image using Gemini 3 Pro
682
- print(f"Reviewing image with {self.review_model}...")
683
- critique, score, needs_improvement = self.review_image(str(iter_path), user_prompt, i, doc_type, iterations)
684
- print(f"✓ Score: {score}/10 (threshold: {threshold}/10)")
685
-
686
- # Save iteration results
687
- iteration_result = {
688
- "iteration": i,
689
- "image_path": str(iter_path),
690
- "prompt": current_prompt,
691
- "critique": critique,
692
- "score": score,
693
- "needs_improvement": needs_improvement,
694
- "success": True,
695
- }
696
- results["iterations"].append(iteration_result)
697
-
698
- # Check if quality is acceptable - STOP EARLY if so
699
- if not needs_improvement:
700
- print(f"\n✓ Quality meets {doc_type} threshold ({score} >= {threshold})")
701
- print(" No further iterations needed!")
702
- results["final_image"] = str(iter_path)
703
- results["final_score"] = score
704
- results["success"] = True
705
- results["early_stop"] = True
706
- results["early_stop_reason"] = f"Quality score {score} meets threshold {threshold} for {doc_type}"
707
- break
708
-
709
- # If this is the last iteration, we're done regardless
710
- if i == iterations:
711
- print("\n⚠ Maximum iterations reached")
712
- results["final_image"] = str(iter_path)
713
- results["final_score"] = score
714
- results["success"] = True
715
- break
716
-
717
- # Quality below threshold - improve prompt for next iteration
718
- print(f"\n⚠ Quality below threshold ({score} < {threshold})")
719
- print("Improving prompt based on feedback...")
720
- current_prompt = self.improve_prompt(user_prompt, critique, i + 1)
721
-
722
- # Copy final version to output path
723
- if results["success"] and results["final_image"]:
724
- final_iter_path = Path(results["final_image"])
725
- if final_iter_path != output_path:
726
- import shutil
727
-
728
- shutil.copy(final_iter_path, output_path)
729
- print(f"\n✓ Final image: {output_path}")
730
-
731
- # Save review log
732
- log_path = output_dir / f"{base_name}_review_log.json"
733
- with open(log_path, "w") as f:
734
- json.dump(results, f, indent=2)
735
- print(f"✓ Review log: {log_path}")
736
-
737
- print(f"\n{'=' * 60}")
738
- print("Generation Complete!")
739
- print(f"Final Score: {results['final_score']}/10")
740
- if results["early_stop"]:
741
- print(
742
- f"Iterations Used: {len([r for r in results['iterations'] if r.get('success')])}/{iterations} (early stop)"
743
- )
744
- print(f"{'=' * 60}\n")
745
-
746
- return results
747
-
748
-
749
- def main():
750
- """Command-line interface."""
751
- parser = argparse.ArgumentParser(
752
- description="Generate scientific schematics using AI with smart iterative refinement",
753
- formatter_class=argparse.RawDescriptionHelpFormatter,
754
- epilog="""
755
- Examples:
756
- # Generate a flowchart for a journal paper
757
- python generate_schematic_ai.py "CONSORT participant flow diagram" -o flowchart.png --doc-type journal
758
-
759
- # Generate neural network architecture for presentation (lower threshold)
760
- python generate_schematic_ai.py "Transformer encoder-decoder architecture" -o transformer.png --doc-type presentation
761
-
762
- # Generate with custom max iterations for poster
763
- python generate_schematic_ai.py "Biological signaling pathway" -o pathway.png --iterations 2 --doc-type poster
764
-
765
- # Verbose output
766
- python generate_schematic_ai.py "Circuit diagram" -o circuit.png -v
767
-
768
- Document Types (quality thresholds):
769
- journal 8.5/10 - Nature, Science, peer-reviewed journals
770
- conference 8.0/10 - Conference papers
771
- thesis 8.0/10 - Dissertations, theses
772
- grant 8.0/10 - Grant proposals
773
- preprint 7.5/10 - arXiv, bioRxiv, etc.
774
- report 7.5/10 - Technical reports
775
- poster 7.0/10 - Academic posters
776
- presentation 6.5/10 - Slides, talks
777
- default 7.5/10 - General purpose
778
-
779
- Note: Multiple iterations only occur if quality is BELOW the threshold.
780
- If the first generation meets the threshold, no extra API calls are made.
781
-
782
- Environment:
783
- OPENROUTER_API_KEY OpenRouter API key (required)
784
- """,
785
- )
786
-
787
- parser.add_argument("prompt", help="Description of the diagram to generate")
788
- parser.add_argument("-o", "--output", required=True, help="Output image path (e.g., diagram.png)")
789
- parser.add_argument("--iterations", type=int, default=2, help="Maximum refinement iterations (default: 2, max: 2)")
790
- parser.add_argument(
791
- "--doc-type",
792
- default="default",
793
- choices=["journal", "conference", "poster", "presentation", "report", "grant", "thesis", "preprint", "default"],
794
- help="Document type for quality threshold (default: default)",
795
- )
796
- parser.add_argument("--api-key", help="OpenRouter API key (or set OPENROUTER_API_KEY)")
797
- parser.add_argument("-v", "--verbose", action="store_true", help="Verbose output")
798
-
799
- args = parser.parse_args()
800
-
801
- # Check for API key
802
- api_key = args.api_key or os.getenv("OPENROUTER_API_KEY")
803
- if not api_key:
804
- print("Error: OPENROUTER_API_KEY environment variable not set")
805
- print("\nSet it with:")
806
- print(" export OPENROUTER_API_KEY='your_api_key'")
807
- print("\nOr provide via --api-key flag")
808
- sys.exit(1)
809
-
810
- # Validate iterations - enforce max of 2
811
- if args.iterations < 1 or args.iterations > 2:
812
- print("Error: Iterations must be between 1 and 2")
813
- sys.exit(1)
814
-
815
- try:
816
- generator = ScientificSchematicGenerator(api_key=api_key, verbose=args.verbose)
817
- results = generator.generate_iterative(
818
- user_prompt=args.prompt, output_path=args.output, iterations=args.iterations, doc_type=args.doc_type
819
- )
820
-
821
- if results["success"]:
822
- print(f"\n✓ Success! Image saved to: {args.output}")
823
- if results.get("early_stop"):
824
- print(
825
- f" (Completed in {len([r for r in results['iterations'] if r.get('success')])} iteration(s) - quality threshold met)"
826
- )
827
- sys.exit(0)
828
- else:
829
- print("\n✗ Generation failed. Check review log for details.")
830
- sys.exit(1)
831
- except Exception as e:
832
- print(f"\n✗ Error: {str(e)}")
833
- sys.exit(1)
834
-
835
-
836
- if __name__ == "__main__":
837
- main()