@synsci/cli-darwin-arm64 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
  44. package/bin/skills/clinical-reports/assets/history_physical_template.md +305 -0
  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
  71. package/bin/skills/hypothesis-generation/assets/FORMATTING_GUIDE.md +672 -0
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  73. package/bin/skills/hypothesis-generation/assets/hypothesis_report_template.tex +572 -0
  74. package/bin/skills/hypothesis-generation/references/experimental_design_patterns.md +329 -0
  75. package/bin/skills/hypothesis-generation/references/hypothesis_quality_criteria.md +198 -0
  76. package/bin/skills/hypothesis-generation/references/literature_search_strategies.md +622 -0
  77. package/bin/skills/latex-posters/README.md +417 -0
  78. package/bin/skills/latex-posters/SKILL.md +1602 -0
  79. package/bin/skills/latex-posters/assets/baposter_template.tex +257 -0
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  81. package/bin/skills/latex-posters/assets/poster_quality_checklist.md +358 -0
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  83. package/bin/skills/latex-posters/references/latex_poster_packages.md +745 -0
  84. package/bin/skills/latex-posters/references/poster_content_guide.md +748 -0
  85. package/bin/skills/latex-posters/references/poster_design_principles.md +806 -0
  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
  96. package/bin/skills/market-research-reports/assets/FORMATTING_GUIDE.md +428 -0
  97. package/bin/skills/market-research-reports/assets/market_report_template.tex +1380 -0
  98. package/bin/skills/market-research-reports/assets/market_research.sty +564 -0
  99. package/bin/skills/market-research-reports/references/data_analysis_patterns.md +548 -0
  100. package/bin/skills/market-research-reports/references/report_structure_guide.md +999 -0
  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
  118. package/bin/skills/ml-paper-writing/references/citation-workflow.md +562 -0
  119. package/bin/skills/ml-paper-writing/references/reviewer-guidelines.md +367 -0
  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
  124. package/bin/skills/ml-paper-writing/templates/aaai2026/aaai2026-unified-supp.tex +144 -0
  125. package/bin/skills/ml-paper-writing/templates/aaai2026/aaai2026-unified-template.tex +952 -0
  126. package/bin/skills/ml-paper-writing/templates/aaai2026/aaai2026.bib +111 -0
  127. package/bin/skills/ml-paper-writing/templates/aaai2026/aaai2026.bst +1493 -0
  128. package/bin/skills/ml-paper-writing/templates/aaai2026/aaai2026.sty +315 -0
  129. package/bin/skills/ml-paper-writing/templates/acl/README.md +50 -0
  130. package/bin/skills/ml-paper-writing/templates/acl/acl.sty +312 -0
  131. package/bin/skills/ml-paper-writing/templates/acl/acl_latex.tex +377 -0
  132. package/bin/skills/ml-paper-writing/templates/acl/acl_lualatex.tex +101 -0
  133. package/bin/skills/ml-paper-writing/templates/acl/acl_natbib.bst +1940 -0
  134. package/bin/skills/ml-paper-writing/templates/acl/anthology.bib.txt +26 -0
  135. package/bin/skills/ml-paper-writing/templates/acl/custom.bib +70 -0
  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
  139. package/bin/skills/ml-paper-writing/templates/colm2025/colm2025_conference.bst +1440 -0
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  142. package/bin/skills/ml-paper-writing/templates/colm2025/colm2025_conference.tex +305 -0
  143. package/bin/skills/ml-paper-writing/templates/colm2025/fancyhdr.sty +485 -0
  144. package/bin/skills/ml-paper-writing/templates/colm2025/math_commands.tex +508 -0
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  146. package/bin/skills/ml-paper-writing/templates/iclr2026/fancyhdr.sty +485 -0
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  167. package/bin/skills/paper-2-web/SKILL.md +491 -0
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  169. package/bin/skills/paper-2-web/references/paper2poster.md +346 -0
  170. package/bin/skills/paper-2-web/references/paper2video.md +305 -0
  171. package/bin/skills/paper-2-web/references/paper2web.md +187 -0
  172. package/bin/skills/paper-2-web/references/usage_examples.md +436 -0
  173. package/bin/skills/peer-review/SKILL.md +702 -0
  174. package/bin/skills/peer-review/references/calibration_guidelines.md +196 -0
  175. package/bin/skills/peer-review/references/common_issues.md +552 -0
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  177. package/bin/skills/peer-review/references/reporting_standards.md +290 -0
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  185. package/bin/skills/research-grants/README.md +285 -0
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  191. package/bin/skills/research-grants/references/darpa_guidelines.md +636 -0
  192. package/bin/skills/research-grants/references/doe_guidelines.md +586 -0
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  339. package/bin/skills/unsloth/references/llms.md +0 -82
@@ -0,0 +1,214 @@
1
+ #!/bin/bash
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+
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+ # Poster PDF Quality Check Script
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+ # Usage: ./review_poster.sh poster.pdf
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+
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+ # Colors for output
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+ RED='\033[0;31m'
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+ GREEN='\033[0;32m'
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+ YELLOW='\033[1;33m'
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+ BLUE='\033[0;34m'
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+ NC='\033[0m' # No Color
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+
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+ # Check if file argument provided
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+ if [ $# -eq 0 ]; then
15
+ echo -e "${RED}Error: No file specified${NC}"
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+ echo "Usage: $0 <poster.pdf>"
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+ exit 1
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+ fi
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+
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+ POSTER_FILE="$1"
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+
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+ # Check if file exists
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+ if [ ! -f "$POSTER_FILE" ]; then
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+ echo -e "${RED}Error: File '$POSTER_FILE' not found${NC}"
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+ exit 1
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+ fi
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+
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+ echo -e "${BLUE}═══════════════════════════════════════════════${NC}"
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+ echo -e "${BLUE} Poster PDF Quality Check${NC}"
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+ echo -e "${BLUE}═══════════════════════════════════════════════${NC}"
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+ echo ""
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+ echo -e "${GREEN}File:${NC} $POSTER_FILE"
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+ echo ""
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+
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+ # Function to check if command exists
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+ command_exists() {
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+ command -v "$1" >/dev/null 2>&1
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+ }
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+
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+ # 1. Page Size Check
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+ echo -e "${YELLOW}[1] Page Dimensions:${NC}"
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+ if command_exists pdfinfo; then
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+ PAGE_SIZE=$(pdfinfo "$POSTER_FILE" 2>/dev/null | grep "Page size")
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+ if [ -n "$PAGE_SIZE" ]; then
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+ echo " $PAGE_SIZE"
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+
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+ # Extract dimensions and check common sizes
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+ WIDTH=$(echo "$PAGE_SIZE" | awk '{print $3}')
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+ HEIGHT=$(echo "$PAGE_SIZE" | awk '{print $5}')
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+
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+ # Check against common poster sizes (approximate)
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+ if [ "$WIDTH" = "2384" ] && [ "$HEIGHT" = "3370" ]; then
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+ echo -e " ${GREEN}✓ Detected: A0 Portrait${NC}"
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+ elif [ "$WIDTH" = "3370" ] && [ "$HEIGHT" = "2384" ]; then
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+ echo -e " ${GREEN}✓ Detected: A0 Landscape${NC}"
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+ elif [ "$WIDTH" = "1684" ] && [ "$HEIGHT" = "2384" ]; then
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+ echo -e " ${GREEN}✓ Detected: A1 Portrait${NC}"
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+ elif [ "$WIDTH" = "2592" ] && [ "$HEIGHT" = "3456" ]; then
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+ echo -e " ${GREEN}✓ Detected: 36×48 inches Portrait${NC}"
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+ else
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+ echo -e " ${YELLOW}⚠ Non-standard size detected${NC}"
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+ fi
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+ else
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+ echo -e " ${RED}✗ Could not extract page size${NC}"
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+ fi
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+ else
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+ echo -e " ${YELLOW}⚠ pdfinfo not installed (install: brew install poppler or apt-get install poppler-utils)${NC}"
68
+ fi
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+ echo ""
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+
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+ # 2. Page Count
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+ echo -e "${YELLOW}[2] Page Count:${NC}"
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+ if command_exists pdfinfo; then
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+ PAGE_COUNT=$(pdfinfo "$POSTER_FILE" 2>/dev/null | grep "Pages" | awk '{print $2}')
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+ if [ "$PAGE_COUNT" = "1" ]; then
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+ echo -e " ${GREEN}✓ Single page (correct for poster)${NC}"
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+ else
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+ echo -e " ${RED}✗ Multiple pages detected: $PAGE_COUNT${NC}"
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+ echo -e " ${YELLOW} Posters should be single page${NC}"
80
+ fi
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+ else
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+ echo -e " ${YELLOW}⚠ pdfinfo not installed${NC}"
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+ fi
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+ echo ""
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+
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+ # 3. File Size
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+ echo -e "${YELLOW}[3] File Size:${NC}"
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+ if command_exists ls; then
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+ FILE_SIZE=$(ls -lh "$POSTER_FILE" | awk '{print $5}')
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+ FILE_SIZE_BYTES=$(ls -l "$POSTER_FILE" | awk '{print $5}')
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+ echo " Size: $FILE_SIZE"
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+
93
+ # Check if file is too large for email
94
+ if [ "$FILE_SIZE_BYTES" -gt 52428800 ]; then # 50MB
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+ echo -e " ${YELLOW}⚠ Large file (>50MB) - may need compression for email${NC}"
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+ echo -e " ${BLUE} Compress with: gs -sDEVICE=pdfwrite -dPDFSETTINGS=/printer -dNOPAUSE -dQUIET -dBATCH -sOutputFile=compressed.pdf $POSTER_FILE${NC}"
97
+ elif [ "$FILE_SIZE_BYTES" -lt 1048576 ]; then # 1MB
98
+ echo -e " ${YELLOW}⚠ Small file - check image quality${NC}"
99
+ else
100
+ echo -e " ${GREEN}✓ Reasonable file size${NC}"
101
+ fi
102
+ fi
103
+ echo ""
104
+
105
+ # 4. Font Embedding Check
106
+ echo -e "${YELLOW}[4] Font Embedding:${NC}"
107
+ if command_exists pdffonts; then
108
+ echo " Checking first 20 fonts..."
109
+ FONT_OUTPUT=$(pdffonts "$POSTER_FILE" 2>/dev/null | head -21)
110
+ echo "$FONT_OUTPUT" | tail -20 | while IFS= read -r line; do
111
+ echo " $line"
112
+ done
113
+
114
+ # Check for non-embedded fonts
115
+ NON_EMBEDDED=$(echo "$FONT_OUTPUT" | tail -n +3 | awk '{if ($4 == "no") print $0}')
116
+ if [ -n "$NON_EMBEDDED" ]; then
117
+ echo -e " ${RED}✗ Some fonts are NOT embedded (printing may fail)${NC}"
118
+ echo -e " ${BLUE} Fix: Recompile with 'pdflatex -dEmbedAllFonts=true poster.tex'${NC}"
119
+ else
120
+ echo -e " ${GREEN}✓ All fonts appear to be embedded${NC}"
121
+ fi
122
+ else
123
+ echo -e " ${YELLOW}⚠ pdffonts not installed (install: brew install poppler or apt-get install poppler-utils)${NC}"
124
+ fi
125
+ echo ""
126
+
127
+ # 5. Image Quality Check
128
+ echo -e "${YELLOW}[5] Image Quality:${NC}"
129
+ if command_exists pdfimages; then
130
+ IMAGE_COUNT=$(pdfimages -list "$POSTER_FILE" 2>/dev/null | tail -n +3 | wc -l | tr -d ' ')
131
+ if [ "$IMAGE_COUNT" -gt 0 ]; then
132
+ echo " Found $IMAGE_COUNT image(s)"
133
+ echo " Image details:"
134
+ pdfimages -list "$POSTER_FILE" 2>/dev/null | head -20
135
+
136
+ # Note: DPI calculation would require page size knowledge
137
+ echo -e " ${BLUE} Verify images are at least 300 DPI for printing${NC}"
138
+ echo -e " ${BLUE} Formula: DPI = pixels / (inches in poster)${NC}"
139
+ else
140
+ echo -e " ${YELLOW}⚠ No images found${NC}"
141
+ fi
142
+ else
143
+ echo -e " ${YELLOW}⚠ pdfimages not installed (install: brew install poppler or apt-get install poppler-utils)${NC}"
144
+ fi
145
+ echo ""
146
+
147
+ # 6. Manual Checks Required
148
+ echo -e "${YELLOW}[6] Manual Visual Inspection Required:${NC}"
149
+ echo ""
150
+ echo -e "${BLUE}Layout and Spacing:${NC}"
151
+ echo " [ ] Content fills entire page (no large white margins)"
152
+ echo " [ ] Consistent spacing between columns"
153
+ echo " [ ] Consistent spacing between blocks/sections"
154
+ echo " [ ] All elements aligned properly"
155
+ echo " [ ] No overlapping text or figures"
156
+ echo ""
157
+
158
+ echo -e "${BLUE}Typography:${NC}"
159
+ echo " [ ] Title visible and large (72pt+)"
160
+ echo " [ ] Section headers readable (48-72pt)"
161
+ echo " [ ] Body text readable (24-36pt minimum)"
162
+ echo " [ ] No text cutoff or running off edges"
163
+ echo " [ ] Consistent font usage"
164
+ echo ""
165
+
166
+ echo -e "${BLUE}Visual Elements:${NC}"
167
+ echo " [ ] All figures display correctly"
168
+ echo " [ ] No pixelated or blurry images"
169
+ echo " [ ] Figure captions present and readable"
170
+ echo " [ ] Colors render as expected"
171
+ echo " [ ] Logos display clearly"
172
+ echo " [ ] QR codes visible and scannable"
173
+ echo ""
174
+
175
+ echo -e "${BLUE}Content:${NC}"
176
+ echo " [ ] All sections present (Intro, Methods, Results, Conclusions)"
177
+ echo " [ ] References included"
178
+ echo " [ ] Contact information visible"
179
+ echo " [ ] No placeholder text (Lorem ipsum, TODO, etc.)"
180
+ echo ""
181
+
182
+ # 7. Recommended Tests
183
+ echo -e "${YELLOW}[7] Recommended Next Steps:${NC}"
184
+ echo ""
185
+ echo -e "${BLUE}Test Print:${NC}"
186
+ echo " • Print at 25% scale (A0→A4, 36×48→Letter)"
187
+ echo " • Check readability from 2-3 feet"
188
+ echo " • Verify colors printed accurately"
189
+ echo ""
190
+
191
+ echo -e "${BLUE}Digital Checks:${NC}"
192
+ echo " • View at 100% zoom in PDF viewer"
193
+ echo " • Test on different screens/devices"
194
+ echo " • Verify QR codes work with scanner app"
195
+ echo ""
196
+
197
+ echo -e "${BLUE}Proofreading:${NC}"
198
+ echo " • Spell-check all text"
199
+ echo " • Verify author names and affiliations"
200
+ echo " • Confirm all statistics and numbers"
201
+ echo " • Ask colleague to review"
202
+ echo ""
203
+
204
+ # 8. Summary
205
+ echo -e "${BLUE}═══════════════════════════════════════════════${NC}"
206
+ echo -e "${BLUE} Quality Check Complete${NC}"
207
+ echo -e "${BLUE}═══════════════════════════════════════════════${NC}"
208
+ echo ""
209
+ echo -e "Review the checks above and complete manual verification."
210
+ echo -e "For full checklist, see: ${BLUE}assets/poster_quality_checklist.md${NC}"
211
+ echo ""
212
+
213
+ exit 0
214
+