@synsci/cli-darwin-x64-baseline 1.1.71 → 1.1.72

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 (339) hide show
  1. package/bin/skills/citation-management/SKILL.md +1109 -0
  2. package/bin/skills/citation-management/assets/bibtex_template.bib +264 -0
  3. package/bin/skills/citation-management/assets/citation_checklist.md +386 -0
  4. package/bin/skills/citation-management/references/bibtex_formatting.md +908 -0
  5. package/bin/skills/citation-management/references/citation_validation.md +794 -0
  6. package/bin/skills/citation-management/references/google_scholar_search.md +725 -0
  7. package/bin/skills/citation-management/references/metadata_extraction.md +870 -0
  8. package/bin/skills/citation-management/references/pubmed_search.md +839 -0
  9. package/bin/skills/citation-management/scripts/doi_to_bibtex.py +182 -0
  10. package/bin/skills/citation-management/scripts/extract_metadata.py +570 -0
  11. package/bin/skills/citation-management/scripts/format_bibtex.py +349 -0
  12. package/bin/skills/citation-management/scripts/search_google_scholar.py +251 -0
  13. package/bin/skills/citation-management/scripts/search_pubmed.py +348 -0
  14. package/bin/skills/citation-management/scripts/validate_citations.py +494 -0
  15. package/bin/skills/clinical-decision-support/README.md +129 -0
  16. package/bin/skills/clinical-decision-support/SKILL.md +506 -0
  17. package/bin/skills/clinical-decision-support/assets/biomarker_report_template.tex +380 -0
  18. package/bin/skills/clinical-decision-support/assets/clinical_pathway_template.tex +222 -0
  19. package/bin/skills/clinical-decision-support/assets/cohort_analysis_template.tex +359 -0
  20. package/bin/skills/clinical-decision-support/assets/color_schemes.tex +149 -0
  21. package/bin/skills/clinical-decision-support/assets/example_gbm_cohort.md +208 -0
  22. package/bin/skills/clinical-decision-support/assets/recommendation_strength_guide.md +328 -0
  23. package/bin/skills/clinical-decision-support/assets/treatment_recommendation_template.tex +529 -0
  24. package/bin/skills/clinical-decision-support/references/biomarker_classification.md +719 -0
  25. package/bin/skills/clinical-decision-support/references/clinical_decision_algorithms.md +604 -0
  26. package/bin/skills/clinical-decision-support/references/evidence_synthesis.md +840 -0
  27. package/bin/skills/clinical-decision-support/references/outcome_analysis.md +640 -0
  28. package/bin/skills/clinical-decision-support/references/patient_cohort_analysis.md +427 -0
  29. package/bin/skills/clinical-decision-support/references/treatment_recommendations.md +521 -0
  30. package/bin/skills/clinical-decision-support/scripts/biomarker_classifier.py +383 -0
  31. package/bin/skills/clinical-decision-support/scripts/build_decision_tree.py +417 -0
  32. package/bin/skills/clinical-decision-support/scripts/create_cohort_tables.py +509 -0
  33. package/bin/skills/clinical-decision-support/scripts/generate_survival_analysis.py +441 -0
  34. package/bin/skills/clinical-decision-support/scripts/validate_cds_document.py +326 -0
  35. package/bin/skills/clinical-reports/IMPLEMENTATION_SUMMARY.md +641 -0
  36. package/bin/skills/clinical-reports/README.md +236 -0
  37. package/bin/skills/clinical-reports/SKILL.md +1127 -0
  38. package/bin/skills/clinical-reports/assets/case_report_template.md +352 -0
  39. package/bin/skills/clinical-reports/assets/clinical_trial_csr_template.md +353 -0
  40. package/bin/skills/clinical-reports/assets/clinical_trial_sae_template.md +359 -0
  41. package/bin/skills/clinical-reports/assets/consult_note_template.md +305 -0
  42. package/bin/skills/clinical-reports/assets/discharge_summary_template.md +453 -0
  43. package/bin/skills/clinical-reports/assets/hipaa_compliance_checklist.md +395 -0
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  45. package/bin/skills/clinical-reports/assets/lab_report_template.md +309 -0
  46. package/bin/skills/clinical-reports/assets/pathology_report_template.md +249 -0
  47. package/bin/skills/clinical-reports/assets/quality_checklist.md +338 -0
  48. package/bin/skills/clinical-reports/assets/radiology_report_template.md +318 -0
  49. package/bin/skills/clinical-reports/assets/soap_note_template.md +253 -0
  50. package/bin/skills/clinical-reports/references/case_report_guidelines.md +570 -0
  51. package/bin/skills/clinical-reports/references/clinical_trial_reporting.md +693 -0
  52. package/bin/skills/clinical-reports/references/data_presentation.md +530 -0
  53. package/bin/skills/clinical-reports/references/diagnostic_reports_standards.md +629 -0
  54. package/bin/skills/clinical-reports/references/medical_terminology.md +588 -0
  55. package/bin/skills/clinical-reports/references/patient_documentation.md +744 -0
  56. package/bin/skills/clinical-reports/references/peer_review_standards.md +585 -0
  57. package/bin/skills/clinical-reports/references/regulatory_compliance.md +577 -0
  58. package/bin/skills/clinical-reports/scripts/check_deidentification.py +332 -0
  59. package/bin/skills/clinical-reports/scripts/compliance_checker.py +78 -0
  60. package/bin/skills/clinical-reports/scripts/extract_clinical_data.py +97 -0
  61. package/bin/skills/clinical-reports/scripts/format_adverse_events.py +97 -0
  62. package/bin/skills/clinical-reports/scripts/generate_report_template.py +149 -0
  63. package/bin/skills/clinical-reports/scripts/terminology_validator.py +126 -0
  64. package/bin/skills/clinical-reports/scripts/validate_case_report.py +323 -0
  65. package/bin/skills/clinical-reports/scripts/validate_trial_report.py +88 -0
  66. package/bin/skills/fireworks-ai/SKILL.md +665 -0
  67. package/bin/skills/generate-image/SKILL.md +178 -0
  68. package/bin/skills/generate-image/scripts/generate_image.py +254 -0
  69. package/bin/skills/groq/SKILL.md +347 -0
  70. package/bin/skills/hypothesis-generation/SKILL.md +293 -0
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  86. package/bin/skills/latex-posters/references/poster_layout_design.md +900 -0
  87. package/bin/skills/latex-posters/scripts/review_poster.sh +214 -0
  88. package/bin/skills/literature-review/SKILL.md +641 -0
  89. package/bin/skills/literature-review/assets/review_template.md +412 -0
  90. package/bin/skills/literature-review/references/citation_styles.md +166 -0
  91. package/bin/skills/literature-review/references/database_strategies.md +455 -0
  92. package/bin/skills/literature-review/scripts/generate_pdf.py +184 -0
  93. package/bin/skills/literature-review/scripts/search_databases.py +310 -0
  94. package/bin/skills/literature-review/scripts/verify_citations.py +218 -0
  95. package/bin/skills/market-research-reports/SKILL.md +904 -0
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  97. package/bin/skills/market-research-reports/assets/market_report_template.tex +1380 -0
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  99. package/bin/skills/market-research-reports/references/data_analysis_patterns.md +548 -0
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  101. package/bin/skills/market-research-reports/references/visual_generation_guide.md +1077 -0
  102. package/bin/skills/market-research-reports/scripts/generate_market_visuals.py +472 -0
  103. package/bin/skills/markitdown/INSTALLATION_GUIDE.md +318 -0
  104. package/bin/skills/markitdown/LICENSE.txt +22 -0
  105. package/bin/skills/markitdown/OPENROUTER_INTEGRATION.md +359 -0
  106. package/bin/skills/markitdown/QUICK_REFERENCE.md +309 -0
  107. package/bin/skills/markitdown/README.md +184 -0
  108. package/bin/skills/markitdown/SKILL.md +486 -0
  109. package/bin/skills/markitdown/SKILL_SUMMARY.md +307 -0
  110. package/bin/skills/markitdown/assets/example_usage.md +463 -0
  111. package/bin/skills/markitdown/references/api_reference.md +399 -0
  112. package/bin/skills/markitdown/references/file_formats.md +542 -0
  113. package/bin/skills/markitdown/scripts/batch_convert.py +195 -0
  114. package/bin/skills/markitdown/scripts/convert_literature.py +262 -0
  115. package/bin/skills/markitdown/scripts/convert_with_ai.py +224 -0
  116. package/bin/skills/ml-paper-writing/SKILL.md +937 -0
  117. package/bin/skills/ml-paper-writing/references/checklists.md +361 -0
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  120. package/bin/skills/ml-paper-writing/references/sources.md +159 -0
  121. package/bin/skills/ml-paper-writing/references/writing-guide.md +476 -0
  122. package/bin/skills/ml-paper-writing/templates/README.md +251 -0
  123. package/bin/skills/ml-paper-writing/templates/aaai2026/README.md +534 -0
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  129. package/bin/skills/ml-paper-writing/templates/acl/README.md +50 -0
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  132. package/bin/skills/ml-paper-writing/templates/acl/acl_lualatex.tex +101 -0
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  134. package/bin/skills/ml-paper-writing/templates/acl/anthology.bib.txt +26 -0
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  136. package/bin/skills/ml-paper-writing/templates/acl/formatting.md +326 -0
  137. package/bin/skills/ml-paper-writing/templates/colm2025/README.md +3 -0
  138. package/bin/skills/ml-paper-writing/templates/colm2025/colm2025_conference.bib +11 -0
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@@ -0,0 +1,243 @@
1
+ #!/usr/bin/env python3
2
+ """
3
+ Test script to verify AI generation implementation.
4
+
5
+ This script performs dry-run tests without making actual API calls.
6
+ It verifies:
7
+ 1. Script structure and imports
8
+ 2. Class initialization
9
+ 3. Method signatures
10
+ 4. Error handling
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+ 5. Command-line interface
12
+
13
+ Usage:
14
+ python test_ai_generation.py
15
+ """
16
+
17
+ import os
18
+ import sys
19
+ from pathlib import Path
20
+
21
+
22
+ # Add scripts directory to path
23
+ scripts_dir = Path(__file__).parent / "scripts"
24
+ sys.path.insert(0, str(scripts_dir))
25
+
26
+
27
+ def test_imports():
28
+ """Test that all required modules can be imported."""
29
+ print("Testing imports...")
30
+ try:
31
+ from generate_schematic_ai import ScientificSchematicGenerator
32
+
33
+ print("✓ generate_schematic_ai imports successfully")
34
+ return True
35
+ except ImportError as e:
36
+ print(f"✗ Import failed: {e}")
37
+ return False
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+
39
+
40
+ def test_class_structure():
41
+ """Test class initialization and structure."""
42
+ print("\nTesting class structure...")
43
+ try:
44
+ from generate_schematic_ai import ScientificSchematicGenerator
45
+
46
+ # Test initialization with dummy key
47
+ generator = ScientificSchematicGenerator(api_key="test_key", verbose=False)
48
+ print("✓ Class initializes successfully")
49
+
50
+ # Check required methods exist
51
+ required_methods = ['generate_image', 'review_image', 'improve_prompt', 'generate_iterative']
52
+
53
+ for method in required_methods:
54
+ if not hasattr(generator, method):
55
+ print(f"✗ Missing method: {method}")
56
+ return False
57
+ print(f"✓ Method exists: {method}")
58
+
59
+ # Check attributes
60
+ if not hasattr(generator, 'api_key'):
61
+ print("✗ Missing attribute: api_key")
62
+ return False
63
+ print("✓ Attribute exists: api_key")
64
+
65
+ if not hasattr(generator, 'image_model'):
66
+ print("✗ Missing attribute: image_model")
67
+ return False
68
+ print(f"✓ Image model: {generator.image_model}")
69
+
70
+ if not hasattr(generator, 'review_model'):
71
+ print("✗ Missing attribute: review_model")
72
+ return False
73
+ print(f"✓ Review model: {generator.review_model}")
74
+
75
+ return True
76
+ except Exception as e:
77
+ print(f"✗ Class structure test failed: {e}")
78
+ return False
79
+
80
+
81
+ def test_error_handling():
82
+ """Test error handling for missing API key."""
83
+ print("\nTesting error handling...")
84
+ try:
85
+ from generate_schematic_ai import ScientificSchematicGenerator
86
+
87
+ # Clear environment variable
88
+ old_key = os.environ.get("OPENROUTER_API_KEY")
89
+ if old_key:
90
+ del os.environ["OPENROUTER_API_KEY"]
91
+
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+ # Try to initialize without key
93
+ try:
94
+ generator = ScientificSchematicGenerator()
95
+ print("✗ Should have raised ValueError for missing API key")
96
+ return False
97
+ except ValueError as e:
98
+ if "OPENROUTER_API_KEY" in str(e):
99
+ print("✓ Correctly raises ValueError for missing API key")
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+ else:
101
+ print(f"✗ Wrong error message: {e}")
102
+ return False
103
+
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+ # Restore environment variable
105
+ if old_key:
106
+ os.environ["OPENROUTER_API_KEY"] = old_key
107
+
108
+ return True
109
+ except Exception as e:
110
+ print(f"✗ Error handling test failed: {e}")
111
+ return False
112
+
113
+
114
+ def test_wrapper_script():
115
+ """Test wrapper script structure."""
116
+ print("\nTesting wrapper script...")
117
+ try:
118
+ import generate_schematic
119
+
120
+ print("✓ generate_schematic imports successfully")
121
+
122
+ # Check main functions exist
123
+ if not hasattr(generate_schematic, 'main'):
124
+ print("✗ Missing function: main")
125
+ return False
126
+ print("✓ Function exists: main")
127
+
128
+ return True
129
+ except Exception as e:
130
+ print(f"✗ Wrapper script test failed: {e}")
131
+ return False
132
+
133
+
134
+ def test_prompt_engineering():
135
+ """Test prompt construction."""
136
+ print("\nTesting prompt engineering...")
137
+ try:
138
+ from generate_schematic_ai import ScientificSchematicGenerator
139
+
140
+ generator = ScientificSchematicGenerator(api_key="test_key", verbose=False)
141
+
142
+ # Test improve_prompt method
143
+ original = "Create a flowchart"
144
+ critique = "Add more spacing between boxes"
145
+ improved = generator.improve_prompt(original, critique, 2)
146
+
147
+ if not improved:
148
+ print("✗ improve_prompt returned empty string")
149
+ return False
150
+
151
+ if original not in improved:
152
+ print("✗ Improved prompt doesn't include original")
153
+ return False
154
+
155
+ if critique not in improved:
156
+ print("✗ Improved prompt doesn't include critique")
157
+ return False
158
+
159
+ if "ITERATION 2" not in improved:
160
+ print("✗ Improved prompt doesn't include iteration number")
161
+ return False
162
+
163
+ print("✓ Prompt engineering works correctly")
164
+ print(f" Original length: {len(original)} chars")
165
+ print(f" Improved length: {len(improved)} chars")
166
+
167
+ return True
168
+ except Exception as e:
169
+ print(f"✗ Prompt engineering test failed: {e}")
170
+ return False
171
+
172
+
173
+ def test_file_paths():
174
+ """Test that all required files exist."""
175
+ print("\nTesting file structure...")
176
+
177
+ base_dir = Path(__file__).parent
178
+ required_files = ["scripts/generate_schematic_ai.py", "scripts/generate_schematic.py", "SKILL.md", "README.md"]
179
+
180
+ all_exist = True
181
+ for file_path in required_files:
182
+ full_path = base_dir / file_path
183
+ if full_path.exists():
184
+ print(f"✓ {file_path}")
185
+ else:
186
+ print(f"✗ Missing: {file_path}")
187
+ all_exist = False
188
+
189
+ return all_exist
190
+
191
+
192
+ def main():
193
+ """Run all tests."""
194
+ print("=" * 60)
195
+ print("Scientific Schematics AI Generation - Verification Tests")
196
+ print("=" * 60)
197
+
198
+ tests = [
199
+ ("File Structure", test_file_paths),
200
+ ("Imports", test_imports),
201
+ ("Class Structure", test_class_structure),
202
+ ("Error Handling", test_error_handling),
203
+ ("Wrapper Script", test_wrapper_script),
204
+ ("Prompt Engineering", test_prompt_engineering),
205
+ ]
206
+
207
+ results = []
208
+ for test_name, test_func in tests:
209
+ try:
210
+ result = test_func()
211
+ results.append((test_name, result))
212
+ except Exception as e:
213
+ print(f"\n✗ Test '{test_name}' crashed: {e}")
214
+ results.append((test_name, False))
215
+
216
+ # Summary
217
+ print("\n" + "=" * 60)
218
+ print("Test Summary")
219
+ print("=" * 60)
220
+
221
+ passed = sum(1 for _, result in results if result)
222
+ total = len(results)
223
+
224
+ for test_name, result in results:
225
+ status = "✓ PASS" if result else "✗ FAIL"
226
+ print(f"{status}: {test_name}")
227
+
228
+ print(f"\nTotal: {passed}/{total} tests passed")
229
+
230
+ if passed == total:
231
+ print("\n✓ All tests passed! Implementation verified.")
232
+ print("\nNext steps:")
233
+ print("1. Set OPENROUTER_API_KEY environment variable")
234
+ print("2. Test with actual API call:")
235
+ print(" python scripts/generate_schematic.py 'test diagram' -o test.png")
236
+ return 0
237
+ else:
238
+ print(f"\n✗ {total - passed} test(s) failed. Please review errors above.")
239
+ return 1
240
+
241
+
242
+ if __name__ == "__main__":
243
+ sys.exit(main())