scientific-writer 2.3.1__py3-none-any.whl

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Files changed (315) hide show
  1. scientific_writer/.claude/WRITER.md +822 -0
  2. scientific_writer/.claude/settings.local.json +30 -0
  3. scientific_writer/.claude/skills/citation-management/SKILL.md +1046 -0
  4. scientific_writer/.claude/skills/citation-management/assets/bibtex_template.bib +264 -0
  5. scientific_writer/.claude/skills/citation-management/assets/citation_checklist.md +386 -0
  6. scientific_writer/.claude/skills/citation-management/references/bibtex_formatting.md +908 -0
  7. scientific_writer/.claude/skills/citation-management/references/citation_validation.md +794 -0
  8. scientific_writer/.claude/skills/citation-management/references/google_scholar_search.md +725 -0
  9. scientific_writer/.claude/skills/citation-management/references/metadata_extraction.md +870 -0
  10. scientific_writer/.claude/skills/citation-management/references/pubmed_search.md +839 -0
  11. scientific_writer/.claude/skills/citation-management/scripts/doi_to_bibtex.py +204 -0
  12. scientific_writer/.claude/skills/citation-management/scripts/extract_metadata.py +569 -0
  13. scientific_writer/.claude/skills/citation-management/scripts/format_bibtex.py +349 -0
  14. scientific_writer/.claude/skills/citation-management/scripts/search_google_scholar.py +282 -0
  15. scientific_writer/.claude/skills/citation-management/scripts/search_pubmed.py +398 -0
  16. scientific_writer/.claude/skills/citation-management/scripts/validate_citations.py +497 -0
  17. scientific_writer/.claude/skills/clinical-reports/IMPLEMENTATION_SUMMARY.md +641 -0
  18. scientific_writer/.claude/skills/clinical-reports/README.md +236 -0
  19. scientific_writer/.claude/skills/clinical-reports/SKILL.md +1088 -0
  20. scientific_writer/.claude/skills/clinical-reports/assets/case_report_template.md +352 -0
  21. scientific_writer/.claude/skills/clinical-reports/assets/clinical_trial_csr_template.md +353 -0
  22. scientific_writer/.claude/skills/clinical-reports/assets/clinical_trial_sae_template.md +359 -0
  23. scientific_writer/.claude/skills/clinical-reports/assets/consult_note_template.md +305 -0
  24. scientific_writer/.claude/skills/clinical-reports/assets/discharge_summary_template.md +453 -0
  25. scientific_writer/.claude/skills/clinical-reports/assets/hipaa_compliance_checklist.md +395 -0
  26. scientific_writer/.claude/skills/clinical-reports/assets/history_physical_template.md +305 -0
  27. scientific_writer/.claude/skills/clinical-reports/assets/lab_report_template.md +309 -0
  28. scientific_writer/.claude/skills/clinical-reports/assets/pathology_report_template.md +249 -0
  29. scientific_writer/.claude/skills/clinical-reports/assets/quality_checklist.md +338 -0
  30. scientific_writer/.claude/skills/clinical-reports/assets/radiology_report_template.md +318 -0
  31. scientific_writer/.claude/skills/clinical-reports/assets/soap_note_template.md +253 -0
  32. scientific_writer/.claude/skills/clinical-reports/references/case_report_guidelines.md +570 -0
  33. scientific_writer/.claude/skills/clinical-reports/references/clinical_trial_reporting.md +693 -0
  34. scientific_writer/.claude/skills/clinical-reports/references/data_presentation.md +530 -0
  35. scientific_writer/.claude/skills/clinical-reports/references/diagnostic_reports_standards.md +629 -0
  36. scientific_writer/.claude/skills/clinical-reports/references/medical_terminology.md +588 -0
  37. scientific_writer/.claude/skills/clinical-reports/references/patient_documentation.md +744 -0
  38. scientific_writer/.claude/skills/clinical-reports/references/peer_review_standards.md +585 -0
  39. scientific_writer/.claude/skills/clinical-reports/references/regulatory_compliance.md +577 -0
  40. scientific_writer/.claude/skills/clinical-reports/scripts/check_deidentification.py +346 -0
  41. scientific_writer/.claude/skills/clinical-reports/scripts/compliance_checker.py +78 -0
  42. scientific_writer/.claude/skills/clinical-reports/scripts/extract_clinical_data.py +102 -0
  43. scientific_writer/.claude/skills/clinical-reports/scripts/format_adverse_events.py +103 -0
  44. scientific_writer/.claude/skills/clinical-reports/scripts/generate_report_template.py +163 -0
  45. scientific_writer/.claude/skills/clinical-reports/scripts/terminology_validator.py +133 -0
  46. scientific_writer/.claude/skills/clinical-reports/scripts/validate_case_report.py +334 -0
  47. scientific_writer/.claude/skills/clinical-reports/scripts/validate_trial_report.py +89 -0
  48. scientific_writer/.claude/skills/document-skills/docx/LICENSE.txt +30 -0
  49. scientific_writer/.claude/skills/document-skills/docx/SKILL.md +197 -0
  50. scientific_writer/.claude/skills/document-skills/docx/docx-js.md +350 -0
  51. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  52. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  53. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  54. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  55. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  56. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  57. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
  58. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
  59. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  60. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  61. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
  62. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
  63. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
  64. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
  65. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
  66. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
  67. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
  68. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
  69. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
  70. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
  71. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
  72. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
  73. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
  74. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
  75. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
  76. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
  77. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
  78. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
  79. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
  80. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
  81. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
  82. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/mce/mc.xsd +75 -0
  83. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
  84. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2012.xsd +67 -0
  85. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2018.xsd +14 -0
  86. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cex-2018.xsd +20 -0
  87. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cid-2016.xsd +13 -0
  88. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
  89. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-symex-2015.xsd +8 -0
  90. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/pack.py +159 -0
  91. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/unpack.py +29 -0
  92. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validate.py +69 -0
  93. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/__init__.py +15 -0
  94. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/base.py +951 -0
  95. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/docx.py +274 -0
  96. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/pptx.py +315 -0
  97. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/redlining.py +279 -0
  98. scientific_writer/.claude/skills/document-skills/docx/ooxml.md +610 -0
  99. scientific_writer/.claude/skills/document-skills/docx/scripts/__init__.py +1 -0
  100. scientific_writer/.claude/skills/document-skills/docx/scripts/document.py +1276 -0
  101. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/comments.xml +3 -0
  102. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsExtended.xml +3 -0
  103. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsExtensible.xml +3 -0
  104. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsIds.xml +3 -0
  105. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/people.xml +3 -0
  106. scientific_writer/.claude/skills/document-skills/docx/scripts/utilities.py +374 -0
  107. scientific_writer/.claude/skills/document-skills/pdf/LICENSE.txt +30 -0
  108. scientific_writer/.claude/skills/document-skills/pdf/SKILL.md +294 -0
  109. scientific_writer/.claude/skills/document-skills/pdf/forms.md +205 -0
  110. scientific_writer/.claude/skills/document-skills/pdf/reference.md +612 -0
  111. scientific_writer/.claude/skills/document-skills/pdf/scripts/check_bounding_boxes.py +70 -0
  112. scientific_writer/.claude/skills/document-skills/pdf/scripts/check_bounding_boxes_test.py +226 -0
  113. scientific_writer/.claude/skills/document-skills/pdf/scripts/check_fillable_fields.py +12 -0
  114. scientific_writer/.claude/skills/document-skills/pdf/scripts/convert_pdf_to_images.py +35 -0
  115. scientific_writer/.claude/skills/document-skills/pdf/scripts/create_validation_image.py +41 -0
  116. scientific_writer/.claude/skills/document-skills/pdf/scripts/extract_form_field_info.py +152 -0
  117. scientific_writer/.claude/skills/document-skills/pdf/scripts/fill_fillable_fields.py +114 -0
  118. scientific_writer/.claude/skills/document-skills/pdf/scripts/fill_pdf_form_with_annotations.py +108 -0
  119. scientific_writer/.claude/skills/document-skills/pptx/LICENSE.txt +30 -0
  120. scientific_writer/.claude/skills/document-skills/pptx/SKILL.md +484 -0
  121. scientific_writer/.claude/skills/document-skills/pptx/html2pptx.md +625 -0
  122. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  123. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  124. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  125. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  126. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  127. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  128. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
  129. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
  130. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  131. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  132. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
  133. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
  134. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
  135. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
  136. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
  137. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
  138. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
  139. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
  140. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
  141. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
  142. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
  143. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
  144. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
  145. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
  146. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
  147. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
  148. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
  149. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
  150. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
  151. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
  152. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
  153. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/mce/mc.xsd +75 -0
  154. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
  155. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2012.xsd +67 -0
  156. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2018.xsd +14 -0
  157. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cex-2018.xsd +20 -0
  158. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cid-2016.xsd +13 -0
  159. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
  160. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-symex-2015.xsd +8 -0
  161. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/pack.py +159 -0
  162. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/unpack.py +29 -0
  163. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validate.py +69 -0
  164. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/__init__.py +15 -0
  165. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/base.py +951 -0
  166. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/docx.py +274 -0
  167. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/pptx.py +315 -0
  168. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/redlining.py +279 -0
  169. scientific_writer/.claude/skills/document-skills/pptx/ooxml.md +427 -0
  170. scientific_writer/.claude/skills/document-skills/pptx/scripts/html2pptx.js +979 -0
  171. scientific_writer/.claude/skills/document-skills/pptx/scripts/inventory.py +1020 -0
  172. scientific_writer/.claude/skills/document-skills/pptx/scripts/rearrange.py +231 -0
  173. scientific_writer/.claude/skills/document-skills/pptx/scripts/replace.py +385 -0
  174. scientific_writer/.claude/skills/document-skills/pptx/scripts/thumbnail.py +450 -0
  175. scientific_writer/.claude/skills/document-skills/xlsx/LICENSE.txt +30 -0
  176. scientific_writer/.claude/skills/document-skills/xlsx/SKILL.md +289 -0
  177. scientific_writer/.claude/skills/document-skills/xlsx/recalc.py +178 -0
  178. scientific_writer/.claude/skills/hypothesis-generation/SKILL.md +155 -0
  179. scientific_writer/.claude/skills/hypothesis-generation/assets/hypothesis_output_template.md +302 -0
  180. scientific_writer/.claude/skills/hypothesis-generation/references/experimental_design_patterns.md +327 -0
  181. scientific_writer/.claude/skills/hypothesis-generation/references/hypothesis_quality_criteria.md +196 -0
  182. scientific_writer/.claude/skills/hypothesis-generation/references/literature_search_strategies.md +505 -0
  183. scientific_writer/.claude/skills/latex-posters/README.md +417 -0
  184. scientific_writer/.claude/skills/latex-posters/SKILL.md +919 -0
  185. scientific_writer/.claude/skills/latex-posters/assets/baposter_template.tex +257 -0
  186. scientific_writer/.claude/skills/latex-posters/assets/beamerposter_template.tex +244 -0
  187. scientific_writer/.claude/skills/latex-posters/assets/poster_quality_checklist.md +358 -0
  188. scientific_writer/.claude/skills/latex-posters/assets/tikzposter_template.tex +251 -0
  189. scientific_writer/.claude/skills/latex-posters/references/latex_poster_packages.md +745 -0
  190. scientific_writer/.claude/skills/latex-posters/references/poster_content_guide.md +748 -0
  191. scientific_writer/.claude/skills/latex-posters/references/poster_design_principles.md +806 -0
  192. scientific_writer/.claude/skills/latex-posters/references/poster_layout_design.md +900 -0
  193. scientific_writer/.claude/skills/latex-posters/scripts/review_poster.sh +214 -0
  194. scientific_writer/.claude/skills/literature-review/SKILL.md +546 -0
  195. scientific_writer/.claude/skills/literature-review/assets/review_template.md +412 -0
  196. scientific_writer/.claude/skills/literature-review/references/citation_styles.md +166 -0
  197. scientific_writer/.claude/skills/literature-review/references/database_strategies.md +381 -0
  198. scientific_writer/.claude/skills/literature-review/scripts/generate_pdf.py +176 -0
  199. scientific_writer/.claude/skills/literature-review/scripts/search_databases.py +303 -0
  200. scientific_writer/.claude/skills/literature-review/scripts/verify_citations.py +222 -0
  201. scientific_writer/.claude/skills/markitdown/INSTALLATION_GUIDE.md +318 -0
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  296. scientific_writer/.claude/skills/venue-templates/assets/journals/plos_one.tex +317 -0
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  311. scientific_writer-2.3.1.dist-info/METADATA +272 -0
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  313. scientific_writer-2.3.1.dist-info/WHEEL +4 -0
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  315. scientific_writer-2.3.1.dist-info/licenses/LICENSE +22 -0
@@ -0,0 +1,214 @@
1
+ #!/bin/bash
2
+
3
+ # Poster PDF Quality Check Script
4
+ # Usage: ./review_poster.sh poster.pdf
5
+
6
+ # Colors for output
7
+ RED='\033[0;31m'
8
+ GREEN='\033[0;32m'
9
+ YELLOW='\033[1;33m'
10
+ BLUE='\033[0;34m'
11
+ NC='\033[0m' # No Color
12
+
13
+ # Check if file argument provided
14
+ if [ $# -eq 0 ]; then
15
+ echo -e "${RED}Error: No file specified${NC}"
16
+ echo "Usage: $0 <poster.pdf>"
17
+ exit 1
18
+ fi
19
+
20
+ POSTER_FILE="$1"
21
+
22
+ # Check if file exists
23
+ if [ ! -f "$POSTER_FILE" ]; then
24
+ echo -e "${RED}Error: File '$POSTER_FILE' not found${NC}"
25
+ exit 1
26
+ fi
27
+
28
+ echo -e "${BLUE}═══════════════════════════════════════════════${NC}"
29
+ echo -e "${BLUE} Poster PDF Quality Check${NC}"
30
+ echo -e "${BLUE}═══════════════════════════════════════════════${NC}"
31
+ echo ""
32
+ echo -e "${GREEN}File:${NC} $POSTER_FILE"
33
+ echo ""
34
+
35
+ # Function to check if command exists
36
+ command_exists() {
37
+ command -v "$1" >/dev/null 2>&1
38
+ }
39
+
40
+ # 1. Page Size Check
41
+ echo -e "${YELLOW}[1] Page Dimensions:${NC}"
42
+ if command_exists pdfinfo; then
43
+ PAGE_SIZE=$(pdfinfo "$POSTER_FILE" 2>/dev/null | grep "Page size")
44
+ if [ -n "$PAGE_SIZE" ]; then
45
+ echo " $PAGE_SIZE"
46
+
47
+ # Extract dimensions and check common sizes
48
+ WIDTH=$(echo "$PAGE_SIZE" | awk '{print $3}')
49
+ HEIGHT=$(echo "$PAGE_SIZE" | awk '{print $5}')
50
+
51
+ # Check against common poster sizes (approximate)
52
+ if [ "$WIDTH" = "2384" ] && [ "$HEIGHT" = "3370" ]; then
53
+ echo -e " ${GREEN}✓ Detected: A0 Portrait${NC}"
54
+ elif [ "$WIDTH" = "3370" ] && [ "$HEIGHT" = "2384" ]; then
55
+ echo -e " ${GREEN}✓ Detected: A0 Landscape${NC}"
56
+ elif [ "$WIDTH" = "1684" ] && [ "$HEIGHT" = "2384" ]; then
57
+ echo -e " ${GREEN}✓ Detected: A1 Portrait${NC}"
58
+ elif [ "$WIDTH" = "2592" ] && [ "$HEIGHT" = "3456" ]; then
59
+ echo -e " ${GREEN}✓ Detected: 36×48 inches Portrait${NC}"
60
+ else
61
+ echo -e " ${YELLOW}⚠ Non-standard size detected${NC}"
62
+ fi
63
+ else
64
+ echo -e " ${RED}✗ Could not extract page size${NC}"
65
+ fi
66
+ else
67
+ echo -e " ${YELLOW}⚠ pdfinfo not installed (install: brew install poppler or apt-get install poppler-utils)${NC}"
68
+ fi
69
+ echo ""
70
+
71
+ # 2. Page Count
72
+ echo -e "${YELLOW}[2] Page Count:${NC}"
73
+ if command_exists pdfinfo; then
74
+ PAGE_COUNT=$(pdfinfo "$POSTER_FILE" 2>/dev/null | grep "Pages" | awk '{print $2}')
75
+ if [ "$PAGE_COUNT" = "1" ]; then
76
+ echo -e " ${GREEN}✓ Single page (correct for poster)${NC}"
77
+ else
78
+ echo -e " ${RED}✗ Multiple pages detected: $PAGE_COUNT${NC}"
79
+ echo -e " ${YELLOW} Posters should be single page${NC}"
80
+ fi
81
+ else
82
+ echo -e " ${YELLOW}⚠ pdfinfo not installed${NC}"
83
+ fi
84
+ echo ""
85
+
86
+ # 3. File Size
87
+ echo -e "${YELLOW}[3] File Size:${NC}"
88
+ if command_exists ls; then
89
+ FILE_SIZE=$(ls -lh "$POSTER_FILE" | awk '{print $5}')
90
+ FILE_SIZE_BYTES=$(ls -l "$POSTER_FILE" | awk '{print $5}')
91
+ echo " Size: $FILE_SIZE"
92
+
93
+ # Check if file is too large for email
94
+ if [ "$FILE_SIZE_BYTES" -gt 52428800 ]; then # 50MB
95
+ echo -e " ${YELLOW}⚠ Large file (>50MB) - may need compression for email${NC}"
96
+ 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
+