scientific-writer 2.1.1__py3-none-any.whl → 2.2.2__py3-none-any.whl

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  1. scientific_writer/.claude/settings.local.json +30 -0
  2. scientific_writer/.claude/skills/citation-management/SKILL.md +1046 -0
  3. scientific_writer/.claude/skills/citation-management/assets/bibtex_template.bib +264 -0
  4. scientific_writer/.claude/skills/citation-management/assets/citation_checklist.md +386 -0
  5. scientific_writer/.claude/skills/citation-management/references/bibtex_formatting.md +908 -0
  6. scientific_writer/.claude/skills/citation-management/references/citation_validation.md +794 -0
  7. scientific_writer/.claude/skills/citation-management/references/google_scholar_search.md +725 -0
  8. scientific_writer/.claude/skills/citation-management/references/metadata_extraction.md +870 -0
  9. scientific_writer/.claude/skills/citation-management/references/pubmed_search.md +839 -0
  10. scientific_writer/.claude/skills/citation-management/scripts/doi_to_bibtex.py +204 -0
  11. scientific_writer/.claude/skills/citation-management/scripts/extract_metadata.py +569 -0
  12. scientific_writer/.claude/skills/citation-management/scripts/format_bibtex.py +349 -0
  13. scientific_writer/.claude/skills/citation-management/scripts/search_google_scholar.py +282 -0
  14. scientific_writer/.claude/skills/citation-management/scripts/search_pubmed.py +398 -0
  15. scientific_writer/.claude/skills/citation-management/scripts/validate_citations.py +497 -0
  16. scientific_writer/.claude/skills/clinical-reports/IMPLEMENTATION_SUMMARY.md +641 -0
  17. scientific_writer/.claude/skills/clinical-reports/README.md +236 -0
  18. scientific_writer/.claude/skills/clinical-reports/SKILL.md +1088 -0
  19. scientific_writer/.claude/skills/clinical-reports/assets/case_report_template.md +352 -0
  20. scientific_writer/.claude/skills/clinical-reports/assets/clinical_trial_csr_template.md +353 -0
  21. scientific_writer/.claude/skills/clinical-reports/assets/clinical_trial_sae_template.md +359 -0
  22. scientific_writer/.claude/skills/clinical-reports/assets/consult_note_template.md +305 -0
  23. scientific_writer/.claude/skills/clinical-reports/assets/discharge_summary_template.md +453 -0
  24. scientific_writer/.claude/skills/clinical-reports/assets/hipaa_compliance_checklist.md +395 -0
  25. scientific_writer/.claude/skills/clinical-reports/assets/history_physical_template.md +305 -0
  26. scientific_writer/.claude/skills/clinical-reports/assets/lab_report_template.md +309 -0
  27. scientific_writer/.claude/skills/clinical-reports/assets/pathology_report_template.md +249 -0
  28. scientific_writer/.claude/skills/clinical-reports/assets/quality_checklist.md +338 -0
  29. scientific_writer/.claude/skills/clinical-reports/assets/radiology_report_template.md +318 -0
  30. scientific_writer/.claude/skills/clinical-reports/assets/soap_note_template.md +253 -0
  31. scientific_writer/.claude/skills/clinical-reports/references/case_report_guidelines.md +570 -0
  32. scientific_writer/.claude/skills/clinical-reports/references/clinical_trial_reporting.md +693 -0
  33. scientific_writer/.claude/skills/clinical-reports/references/data_presentation.md +530 -0
  34. scientific_writer/.claude/skills/clinical-reports/references/diagnostic_reports_standards.md +629 -0
  35. scientific_writer/.claude/skills/clinical-reports/references/medical_terminology.md +588 -0
  36. scientific_writer/.claude/skills/clinical-reports/references/patient_documentation.md +744 -0
  37. scientific_writer/.claude/skills/clinical-reports/references/peer_review_standards.md +585 -0
  38. scientific_writer/.claude/skills/clinical-reports/references/regulatory_compliance.md +577 -0
  39. scientific_writer/.claude/skills/clinical-reports/scripts/check_deidentification.py +346 -0
  40. scientific_writer/.claude/skills/clinical-reports/scripts/compliance_checker.py +78 -0
  41. scientific_writer/.claude/skills/clinical-reports/scripts/extract_clinical_data.py +102 -0
  42. scientific_writer/.claude/skills/clinical-reports/scripts/format_adverse_events.py +103 -0
  43. scientific_writer/.claude/skills/clinical-reports/scripts/generate_report_template.py +163 -0
  44. scientific_writer/.claude/skills/clinical-reports/scripts/terminology_validator.py +133 -0
  45. scientific_writer/.claude/skills/clinical-reports/scripts/validate_case_report.py +334 -0
  46. scientific_writer/.claude/skills/clinical-reports/scripts/validate_trial_report.py +89 -0
  47. scientific_writer/.claude/skills/document-skills/docx/LICENSE.txt +30 -0
  48. scientific_writer/.claude/skills/document-skills/docx/SKILL.md +197 -0
  49. scientific_writer/.claude/skills/document-skills/docx/docx-js.md +350 -0
  50. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  51. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  52. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  53. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  54. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  55. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  56. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
  57. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
  58. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  59. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  60. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
  61. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
  62. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
  63. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
  64. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
  65. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
  66. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
  67. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
  68. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
  69. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
  70. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
  71. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
  72. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
  73. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
  74. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
  75. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
  76. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
  77. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
  78. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
  79. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
  80. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
  81. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/mce/mc.xsd +75 -0
  82. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
  83. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2012.xsd +67 -0
  84. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2018.xsd +14 -0
  85. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cex-2018.xsd +20 -0
  86. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cid-2016.xsd +13 -0
  87. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
  88. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-symex-2015.xsd +8 -0
  89. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/pack.py +159 -0
  90. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/unpack.py +29 -0
  91. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validate.py +69 -0
  92. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/__init__.py +15 -0
  93. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/base.py +951 -0
  94. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/docx.py +274 -0
  95. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/pptx.py +315 -0
  96. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/redlining.py +279 -0
  97. scientific_writer/.claude/skills/document-skills/docx/ooxml.md +610 -0
  98. scientific_writer/.claude/skills/document-skills/docx/scripts/__init__.py +1 -0
  99. scientific_writer/.claude/skills/document-skills/docx/scripts/document.py +1276 -0
  100. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/comments.xml +3 -0
  101. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsExtended.xml +3 -0
  102. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsExtensible.xml +3 -0
  103. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsIds.xml +3 -0
  104. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/people.xml +3 -0
  105. scientific_writer/.claude/skills/document-skills/docx/scripts/utilities.py +374 -0
  106. scientific_writer/.claude/skills/document-skills/pdf/LICENSE.txt +30 -0
  107. scientific_writer/.claude/skills/document-skills/pdf/SKILL.md +294 -0
  108. scientific_writer/.claude/skills/document-skills/pdf/forms.md +205 -0
  109. scientific_writer/.claude/skills/document-skills/pdf/reference.md +612 -0
  110. scientific_writer/.claude/skills/document-skills/pdf/scripts/check_bounding_boxes.py +70 -0
  111. scientific_writer/.claude/skills/document-skills/pdf/scripts/check_bounding_boxes_test.py +226 -0
  112. scientific_writer/.claude/skills/document-skills/pdf/scripts/check_fillable_fields.py +12 -0
  113. scientific_writer/.claude/skills/document-skills/pdf/scripts/convert_pdf_to_images.py +35 -0
  114. scientific_writer/.claude/skills/document-skills/pdf/scripts/create_validation_image.py +41 -0
  115. scientific_writer/.claude/skills/document-skills/pdf/scripts/extract_form_field_info.py +152 -0
  116. scientific_writer/.claude/skills/document-skills/pdf/scripts/fill_fillable_fields.py +114 -0
  117. scientific_writer/.claude/skills/document-skills/pdf/scripts/fill_pdf_form_with_annotations.py +108 -0
  118. scientific_writer/.claude/skills/document-skills/pptx/LICENSE.txt +30 -0
  119. scientific_writer/.claude/skills/document-skills/pptx/SKILL.md +484 -0
  120. scientific_writer/.claude/skills/document-skills/pptx/html2pptx.md +625 -0
  121. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  122. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  123. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  124. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  125. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  126. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  127. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
  128. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
  129. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  130. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  131. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
  132. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
  133. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
  134. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
  135. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
  136. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
  137. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
  138. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
  139. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
  140. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
  141. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
  142. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
  143. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
  144. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
  145. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
  146. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
  147. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
  148. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
  149. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
  150. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
  151. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
  152. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/mce/mc.xsd +75 -0
  153. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
  154. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2012.xsd +67 -0
  155. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2018.xsd +14 -0
  156. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cex-2018.xsd +20 -0
  157. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cid-2016.xsd +13 -0
  158. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
  159. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-symex-2015.xsd +8 -0
  160. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/pack.py +159 -0
  161. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/unpack.py +29 -0
  162. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validate.py +69 -0
  163. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/__init__.py +15 -0
  164. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/base.py +951 -0
  165. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/docx.py +274 -0
  166. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/pptx.py +315 -0
  167. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/redlining.py +279 -0
  168. scientific_writer/.claude/skills/document-skills/pptx/ooxml.md +427 -0
  169. scientific_writer/.claude/skills/document-skills/pptx/scripts/html2pptx.js +979 -0
  170. scientific_writer/.claude/skills/document-skills/pptx/scripts/inventory.py +1020 -0
  171. scientific_writer/.claude/skills/document-skills/pptx/scripts/rearrange.py +231 -0
  172. scientific_writer/.claude/skills/document-skills/pptx/scripts/replace.py +385 -0
  173. scientific_writer/.claude/skills/document-skills/pptx/scripts/thumbnail.py +450 -0
  174. scientific_writer/.claude/skills/document-skills/xlsx/LICENSE.txt +30 -0
  175. scientific_writer/.claude/skills/document-skills/xlsx/SKILL.md +289 -0
  176. scientific_writer/.claude/skills/document-skills/xlsx/recalc.py +178 -0
  177. scientific_writer/.claude/skills/hypothesis-generation/SKILL.md +155 -0
  178. scientific_writer/.claude/skills/hypothesis-generation/assets/hypothesis_output_template.md +302 -0
  179. scientific_writer/.claude/skills/hypothesis-generation/references/experimental_design_patterns.md +327 -0
  180. scientific_writer/.claude/skills/hypothesis-generation/references/hypothesis_quality_criteria.md +196 -0
  181. scientific_writer/.claude/skills/hypothesis-generation/references/literature_search_strategies.md +505 -0
  182. scientific_writer/.claude/skills/latex-posters/README.md +417 -0
  183. scientific_writer/.claude/skills/latex-posters/SKILL.md +919 -0
  184. scientific_writer/.claude/skills/latex-posters/assets/baposter_template.tex +257 -0
  185. scientific_writer/.claude/skills/latex-posters/assets/beamerposter_template.tex +244 -0
  186. scientific_writer/.claude/skills/latex-posters/assets/poster_quality_checklist.md +358 -0
  187. scientific_writer/.claude/skills/latex-posters/assets/tikzposter_template.tex +251 -0
  188. scientific_writer/.claude/skills/latex-posters/references/latex_poster_packages.md +745 -0
  189. scientific_writer/.claude/skills/latex-posters/references/poster_content_guide.md +748 -0
  190. scientific_writer/.claude/skills/latex-posters/references/poster_design_principles.md +806 -0
  191. scientific_writer/.claude/skills/latex-posters/references/poster_layout_design.md +900 -0
  192. scientific_writer/.claude/skills/latex-posters/scripts/review_poster.sh +214 -0
  193. scientific_writer/.claude/skills/literature-review/SKILL.md +546 -0
  194. scientific_writer/.claude/skills/literature-review/assets/review_template.md +412 -0
  195. scientific_writer/.claude/skills/literature-review/references/citation_styles.md +166 -0
  196. scientific_writer/.claude/skills/literature-review/references/database_strategies.md +381 -0
  197. scientific_writer/.claude/skills/literature-review/scripts/generate_pdf.py +176 -0
  198. scientific_writer/.claude/skills/literature-review/scripts/search_databases.py +303 -0
  199. scientific_writer/.claude/skills/literature-review/scripts/verify_citations.py +222 -0
  200. scientific_writer/.claude/skills/markitdown/INSTALLATION_GUIDE.md +318 -0
  201. scientific_writer/.claude/skills/markitdown/LICENSE.txt +22 -0
  202. scientific_writer/.claude/skills/markitdown/OPENROUTER_INTEGRATION.md +359 -0
  203. scientific_writer/.claude/skills/markitdown/QUICK_REFERENCE.md +309 -0
  204. scientific_writer/.claude/skills/markitdown/README.md +184 -0
  205. scientific_writer/.claude/skills/markitdown/SKILL.md +450 -0
  206. scientific_writer/.claude/skills/markitdown/SKILL_SUMMARY.md +307 -0
  207. scientific_writer/.claude/skills/markitdown/assets/example_usage.md +463 -0
  208. scientific_writer/.claude/skills/markitdown/references/api_reference.md +399 -0
  209. scientific_writer/.claude/skills/markitdown/references/file_formats.md +542 -0
  210. scientific_writer/.claude/skills/markitdown/scripts/batch_convert.py +228 -0
  211. scientific_writer/.claude/skills/markitdown/scripts/convert_literature.py +283 -0
  212. scientific_writer/.claude/skills/markitdown/scripts/convert_with_ai.py +243 -0
  213. scientific_writer/.claude/skills/paper-2-web/SKILL.md +455 -0
  214. scientific_writer/.claude/skills/paper-2-web/references/installation.md +141 -0
  215. scientific_writer/.claude/skills/paper-2-web/references/paper2poster.md +346 -0
  216. scientific_writer/.claude/skills/paper-2-web/references/paper2video.md +305 -0
  217. scientific_writer/.claude/skills/paper-2-web/references/paper2web.md +187 -0
  218. scientific_writer/.claude/skills/paper-2-web/references/usage_examples.md +436 -0
  219. scientific_writer/.claude/skills/peer-review/SKILL.md +375 -0
  220. scientific_writer/.claude/skills/peer-review/references/common_issues.md +552 -0
  221. scientific_writer/.claude/skills/peer-review/references/reporting_standards.md +290 -0
  222. scientific_writer/.claude/skills/research-grants/README.md +285 -0
  223. scientific_writer/.claude/skills/research-grants/SKILL.md +896 -0
  224. scientific_writer/.claude/skills/research-grants/assets/budget_justification_template.md +453 -0
  225. scientific_writer/.claude/skills/research-grants/assets/nih_specific_aims_template.md +166 -0
  226. scientific_writer/.claude/skills/research-grants/assets/nsf_project_summary_template.md +92 -0
  227. scientific_writer/.claude/skills/research-grants/references/broader_impacts.md +392 -0
  228. scientific_writer/.claude/skills/research-grants/references/darpa_guidelines.md +636 -0
  229. scientific_writer/.claude/skills/research-grants/references/doe_guidelines.md +586 -0
  230. scientific_writer/.claude/skills/research-grants/references/nih_guidelines.md +851 -0
  231. scientific_writer/.claude/skills/research-grants/references/nsf_guidelines.md +570 -0
  232. scientific_writer/.claude/skills/research-grants/references/specific_aims_guide.md +458 -0
  233. scientific_writer/.claude/skills/research-lookup/README.md +116 -0
  234. scientific_writer/.claude/skills/research-lookup/SKILL.md +443 -0
  235. scientific_writer/.claude/skills/research-lookup/examples.py +174 -0
  236. scientific_writer/.claude/skills/research-lookup/lookup.py +93 -0
  237. scientific_writer/.claude/skills/research-lookup/research_lookup.py +335 -0
  238. scientific_writer/.claude/skills/research-lookup/scripts/research_lookup.py +261 -0
  239. scientific_writer/.claude/skills/scholar-evaluation/SKILL.md +254 -0
  240. scientific_writer/.claude/skills/scholar-evaluation/references/evaluation_framework.md +663 -0
  241. scientific_writer/.claude/skills/scholar-evaluation/scripts/calculate_scores.py +378 -0
  242. scientific_writer/.claude/skills/scientific-critical-thinking/SKILL.md +530 -0
  243. scientific_writer/.claude/skills/scientific-critical-thinking/references/common_biases.md +364 -0
  244. scientific_writer/.claude/skills/scientific-critical-thinking/references/evidence_hierarchy.md +484 -0
  245. scientific_writer/.claude/skills/scientific-critical-thinking/references/experimental_design.md +496 -0
  246. scientific_writer/.claude/skills/scientific-critical-thinking/references/logical_fallacies.md +478 -0
  247. scientific_writer/.claude/skills/scientific-critical-thinking/references/scientific_method.md +169 -0
  248. scientific_writer/.claude/skills/scientific-critical-thinking/references/statistical_pitfalls.md +506 -0
  249. scientific_writer/.claude/skills/scientific-schematics/SKILL.md +2035 -0
  250. scientific_writer/.claude/skills/scientific-schematics/assets/block_diagram_template.tex +199 -0
  251. scientific_writer/.claude/skills/scientific-schematics/assets/circuit_template.tex +159 -0
  252. scientific_writer/.claude/skills/scientific-schematics/assets/flowchart_template.tex +161 -0
  253. scientific_writer/.claude/skills/scientific-schematics/assets/pathway_template.tex +162 -0
  254. scientific_writer/.claude/skills/scientific-schematics/assets/tikz_styles.tex +422 -0
  255. scientific_writer/.claude/skills/scientific-schematics/references/best_practices.md +562 -0
  256. scientific_writer/.claude/skills/scientific-schematics/references/diagram_types.md +637 -0
  257. scientific_writer/.claude/skills/scientific-schematics/references/python_libraries.md +791 -0
  258. scientific_writer/.claude/skills/scientific-schematics/references/tikz_guide.md +734 -0
  259. scientific_writer/.claude/skills/scientific-schematics/scripts/circuit_generator.py +307 -0
  260. scientific_writer/.claude/skills/scientific-schematics/scripts/compile_tikz.py +292 -0
  261. scientific_writer/.claude/skills/scientific-schematics/scripts/generate_flowchart.py +281 -0
  262. scientific_writer/.claude/skills/scientific-schematics/scripts/pathway_diagram.py +406 -0
  263. scientific_writer/.claude/skills/scientific-writing/SKILL.md +443 -0
  264. scientific_writer/.claude/skills/scientific-writing/references/citation_styles.md +720 -0
  265. scientific_writer/.claude/skills/scientific-writing/references/figures_tables.md +806 -0
  266. scientific_writer/.claude/skills/scientific-writing/references/imrad_structure.md +658 -0
  267. scientific_writer/.claude/skills/scientific-writing/references/reporting_guidelines.md +748 -0
  268. scientific_writer/.claude/skills/scientific-writing/references/writing_principles.md +824 -0
  269. scientific_writer/.claude/skills/treatment-plans/README.md +483 -0
  270. scientific_writer/.claude/skills/treatment-plans/SKILL.md +817 -0
  271. scientific_writer/.claude/skills/treatment-plans/assets/chronic_disease_management_plan.tex +636 -0
  272. scientific_writer/.claude/skills/treatment-plans/assets/general_medical_treatment_plan.tex +616 -0
  273. scientific_writer/.claude/skills/treatment-plans/assets/mental_health_treatment_plan.tex +745 -0
  274. scientific_writer/.claude/skills/treatment-plans/assets/pain_management_plan.tex +770 -0
  275. scientific_writer/.claude/skills/treatment-plans/assets/perioperative_care_plan.tex +724 -0
  276. scientific_writer/.claude/skills/treatment-plans/assets/quality_checklist.md +471 -0
  277. scientific_writer/.claude/skills/treatment-plans/assets/rehabilitation_treatment_plan.tex +727 -0
  278. scientific_writer/.claude/skills/treatment-plans/references/goal_setting_frameworks.md +411 -0
  279. scientific_writer/.claude/skills/treatment-plans/references/intervention_guidelines.md +507 -0
  280. scientific_writer/.claude/skills/treatment-plans/references/regulatory_compliance.md +476 -0
  281. scientific_writer/.claude/skills/treatment-plans/references/specialty_specific_guidelines.md +607 -0
  282. scientific_writer/.claude/skills/treatment-plans/references/treatment_plan_standards.md +456 -0
  283. scientific_writer/.claude/skills/treatment-plans/scripts/check_completeness.py +318 -0
  284. scientific_writer/.claude/skills/treatment-plans/scripts/generate_template.py +244 -0
  285. scientific_writer/.claude/skills/treatment-plans/scripts/timeline_generator.py +369 -0
  286. scientific_writer/.claude/skills/treatment-plans/scripts/validate_treatment_plan.py +367 -0
  287. scientific_writer/.claude/skills/venue-templates/SKILL.md +590 -0
  288. scientific_writer/.claude/skills/venue-templates/assets/grants/nih_specific_aims.tex +235 -0
  289. scientific_writer/.claude/skills/venue-templates/assets/grants/nsf_proposal_template.tex +375 -0
  290. scientific_writer/.claude/skills/venue-templates/assets/journals/nature_article.tex +171 -0
  291. scientific_writer/.claude/skills/venue-templates/assets/journals/neurips_article.tex +283 -0
  292. scientific_writer/.claude/skills/venue-templates/assets/journals/plos_one.tex +317 -0
  293. scientific_writer/.claude/skills/venue-templates/assets/posters/beamerposter_academic.tex +311 -0
  294. scientific_writer/.claude/skills/venue-templates/references/conferences_formatting.md +564 -0
  295. scientific_writer/.claude/skills/venue-templates/references/grants_requirements.md +787 -0
  296. scientific_writer/.claude/skills/venue-templates/references/journals_formatting.md +486 -0
  297. scientific_writer/.claude/skills/venue-templates/references/posters_guidelines.md +628 -0
  298. scientific_writer/.claude/skills/venue-templates/scripts/customize_template.py +206 -0
  299. scientific_writer/.claude/skills/venue-templates/scripts/query_template.py +260 -0
  300. scientific_writer/.claude/skills/venue-templates/scripts/validate_format.py +255 -0
  301. scientific_writer/CLAUDE.md +748 -0
  302. scientific_writer/__init__.py +2 -2
  303. scientific_writer/api.py +14 -7
  304. scientific_writer/cli.py +12 -7
  305. scientific_writer/core.py +27 -5
  306. {scientific_writer-2.1.1.dist-info → scientific_writer-2.2.2.dist-info}/METADATA +5 -1
  307. scientific_writer-2.2.2.dist-info/RECORD +312 -0
  308. scientific_writer-2.1.1.dist-info/RECORD +0 -11
  309. {scientific_writer-2.1.1.dist-info → scientific_writer-2.2.2.dist-info}/WHEEL +0 -0
  310. {scientific_writer-2.1.1.dist-info → scientific_writer-2.2.2.dist-info}/entry_points.txt +0 -0
  311. {scientific_writer-2.1.1.dist-info → scientific_writer-2.2.2.dist-info}/licenses/LICENSE +0 -0
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+ # Paper2Video: Presentation Video Generation
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+
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+ ## Overview
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+
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+ Paper2Video generates presentation videos from LaTeX sources, transforming academic papers into engaging video presentations. The system processes papers through multiple specialized modules to create professional presentation videos complete with slides, narration, and optional talking-head video.
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+
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+ ## Core Components
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+
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+ ### 1. Slide Generation Module
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+ - Extracts key content from paper structure
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+ - Creates visually appealing presentation slides
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+ - Organizes content in logical flow
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+ - Includes figures, tables, and equations
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+ - Optimizes text density for readability
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+
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+ ### 2. Subtitle Generation Module
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+ - Generates natural presentation script
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+ - Synchronizes text with slide transitions
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+ - Creates speaker notes and timing
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+ - Supports multiple languages
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+ - Optimizes for speech synthesis
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+
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+ ### 3. Speech Synthesis Module
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+ - Converts subtitles to natural-sounding speech
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+ - Supports multiple voices and accents
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+ - Controls pacing and emphasis
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+ - Generates audio track for video
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+ - Handles technical terminology
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+
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+ ### 4. Cursor Movement Module
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+ - Simulates presenter cursor movements
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+ - Highlights key points on slides
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+ - Guides viewer attention
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+ - Creates natural presentation flow
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+ - Synchronizes with narration
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+
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+ ### 5. Talking-Head Video Generation (Optional)
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+ - Uses Hallo2 for realistic presenter video
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+ - Lip-syncs with generated audio
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+ - Requires reference image or video
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+ - GPU-intensive (NVIDIA A6000 48GB minimum)
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+ - Creates engaging presenter presence
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+
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+ ## Usage
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+
46
+ ### Basic Video Generation (Without Talking-Head)
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+
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+ ```bash
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+ python pipeline_light.py \
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+ --model_name_t gpt-4.1 \
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+ --model_name_v gpt-4.1 \
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+ --result_dir /path/to/output \
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+ --paper_latex_root /path/to/paper
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+ ```
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+
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+ ### Full Video Generation (With Talking-Head)
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+
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+ ```bash
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+ python pipeline_all.py \
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+ --input-dir "path/to/papers" \
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+ --output-dir "path/to/output" \
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+ --model-choice 1 \
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+ --enable-talking-head
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+ ```
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+
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+ ### Parameters
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+
68
+ **Model Configuration:**
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+ - `--model_name_t`: Model for text/subtitle generation (default: gpt-4.1)
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+ - `--model_name_v`: Model for visual/slide generation (default: gpt-4.1)
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+ - `--model-choice`: Preset model configuration (1=GPT-4, 2=GPT-4.1)
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+
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+ **Input/Output:**
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+ - `--paper_latex_root`: Root directory of LaTeX paper source
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+ - `--result_dir` or `--output-dir`: Output directory for generated videos
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+ - `--input-dir`: Directory containing multiple papers to process
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+
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+ **Video Options:**
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+ - `--enable-talking-head`: Enable talking-head video generation (requires GPU)
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+ - `--video-duration`: Target video duration in seconds (default: auto-calculated)
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+ - `--slides-per-minute`: Control presentation pacing (default: 2-3)
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+ - `--voice`: Voice selection for speech synthesis
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+
84
+ **Quality Settings:**
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+ - `--video-resolution`: Output resolution (default: 1920x1080)
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+ - `--video-fps`: Frame rate (default: 30)
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+ - `--audio-quality`: Audio bitrate (default: 192kbps)
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+
89
+ ## Input Requirements
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+
91
+ ### LaTeX Source Structure
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+ ```
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+ paper_directory/
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+ ├── main.tex # Main paper file
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+ ├── sections/ # Section files (if split)
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+ │ ├── introduction.tex
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+ │ ├── methods.tex
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+ │ └── results.tex
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+ ├── figures/ # Figure files
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+ │ ├── fig1.pdf
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+ │ ├── fig2.png
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+ │ └── ...
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+ ├── tables/ # Table files
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+ └── bibliography.bib # References
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+ ```
106
+
107
+ ### Required Elements
108
+ - Valid LaTeX source that compiles
109
+ - Proper section structure (abstract, introduction, methods, results, conclusion)
110
+ - High-quality figures (vector formats preferred)
111
+ - Complete bibliography
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+
113
+ ### Optional Elements
114
+ - Author photos for talking-head generation
115
+ - Custom slide templates
116
+ - Background music or sound effects
117
+ - Institution branding assets
118
+
119
+ ## Output Structure
120
+
121
+ ```
122
+ output/paper_name/video/
123
+ ├── final_video.mp4 # Complete presentation video
124
+ ├── slides/ # Generated slide images
125
+ │ ├── slide_001.png
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+ │ ├── slide_002.png
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+ │ └── ...
128
+ ├── audio/ # Audio components
129
+ │ ├── narration.mp3 # Speech synthesis output
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+ │ └── background.mp3 # Optional background audio
131
+ ├── subtitles/ # Subtitle files
132
+ │ ├── subtitles.srt # Standard subtitle format
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+ │ └── subtitles.vtt # WebVTT format
134
+ ├── script/ # Presentation script
135
+ │ ├── full_script.txt # Complete narration text
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+ │ └── slide_notes.json # Slide-by-slide notes
137
+ └── metadata/ # Video metadata
138
+ ├── timings.json # Slide timing information
139
+ └── video_info.json # Video properties
140
+ ```
141
+
142
+ ## Video Generation Process
143
+
144
+ ### Phase 1: Content Analysis
145
+ 1. Parse LaTeX source structure
146
+ 2. Extract key concepts and findings
147
+ 3. Identify important figures and equations
148
+ 4. Determine logical presentation flow
149
+
150
+ ### Phase 2: Slide Creation
151
+ 1. Design slide layouts based on content
152
+ 2. Allocate content across appropriate number of slides
153
+ 3. Incorporate figures and visual elements
154
+ 4. Apply consistent styling and branding
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+
156
+ ### Phase 3: Script Generation
157
+ 1. Write natural presentation narration
158
+ 2. Time script sections to slides
159
+ 3. Add transitions and emphasis
160
+ 4. Optimize for speech synthesis
161
+
162
+ ### Phase 4: Audio Production
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+ 1. Generate speech from script
164
+ 2. Add emphasis and pacing
165
+ 3. Include pauses for slide transitions
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+ 4. Mix with optional background audio
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+
168
+ ### Phase 5: Video Assembly
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+ 1. Combine slides with timing information
170
+ 2. Synchronize audio track
171
+ 3. Add cursor movements and highlights
172
+ 4. Generate talking-head video (if enabled)
173
+ 5. Render final video file
174
+
175
+ ## Customization Options
176
+
177
+ ### Presentation Style
178
+ - **Academic**: Formal, detailed, comprehensive
179
+ - **Conference**: Focused on key findings, faster pace
180
+ - **Public**: Simplified language, engaging storytelling
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+ - **Tutorial**: Step-by-step explanation, educational focus
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+
183
+ ### Voice Configuration
184
+ Available voice options (via speech synthesis):
185
+ - Multiple languages and accents
186
+ - Male/female voice selection
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+ - Speaking rate adjustment
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+ - Pitch and tone customization
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+
190
+ ### Visual Themes
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+ - Institution branding colors
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+ - Conference template matching
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+ - Custom backgrounds and fonts
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+ - Dark mode presentations
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+
196
+ ## Quality Assessment
197
+
198
+ ### Content Quality Metrics
199
+ - **Completeness**: Coverage of paper content
200
+ - **Clarity**: Explanation quality and coherence
201
+ - **Flow**: Logical progression of ideas
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+ - **Engagement**: Visual appeal and pacing
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+
204
+ ### Technical Quality Metrics
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+ - **Audio quality**: Speech clarity and naturalness
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+ - **Video quality**: Resolution and encoding
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+ - **Synchronization**: Audio-visual alignment
208
+ - **Timing**: Appropriate slide duration
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+
210
+ ## Advanced Features
211
+
212
+ ### Multi-Language Support
213
+ - Generate presentations in multiple languages
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+ - Automatic translation of script
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+ - Language-appropriate voice selection
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+ - Cultural adaptation of presentation style
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+
218
+ ### Talking-Head Generation with Hallo2
219
+ Requires:
220
+ - NVIDIA A6000 GPU (48GB minimum)
221
+ - Reference image or short video of presenter
222
+ - Additional processing time (2-3x longer)
223
+
224
+ Benefits:
225
+ - More engaging presentation
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+ - Professional presenter appearance
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+ - Natural gestures and expressions
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+ - Lip-sync accuracy
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+
230
+ ### Interactive Elements
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+ - Embedded clickable links
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+ - Navigation menu
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+ - Chapter markers
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+ - Supplementary material links
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+
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+ ## Best Practices
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+
238
+ ### Input Preparation
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+ 1. **Clean LaTeX source**: Remove unnecessary comments and artifacts
240
+ 2. **High-quality figures**: Use vector formats when possible
241
+ 3. **Clear structure**: Well-organized sections and subsections
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+ 4. **Complete content**: Include all necessary files and references
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+
244
+ ### Model Selection
245
+ - **Text generation (model_name_t)**: GPT-4.1 for best script quality
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+ - **Visual generation (model_name_v)**: GPT-4.1 for optimal slide design
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+ - For faster processing with acceptable quality: GPT-3.5-turbo
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+
249
+ ### Video Optimization
250
+ 1. **Target duration**: 10-15 minutes for conference talks, 30-45 for detailed presentations
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+ 2. **Pacing**: 2-3 slides per minute for technical content
252
+ 3. **Resolution**: 1920x1080 for standard, 3840x2160 for high-quality
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+ 4. **Audio**: 192kbps minimum for clear speech
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+
255
+ ### Quality Review
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+ Before finalizing:
257
+ 1. Watch entire video for content accuracy
258
+ 2. Check audio synchronization with slides
259
+ 3. Verify figure quality and readability
260
+ 4. Test subtitle accuracy and timing
261
+ 5. Review cursor movements for natural flow
262
+
263
+ ## Performance Considerations
264
+
265
+ ### Processing Time
266
+ - **Without talking-head**: 10-30 minutes per paper (depending on length)
267
+ - **With talking-head**: 30-120 minutes per paper
268
+ - **Factors**: Paper length, figure count, model speed, GPU availability
269
+
270
+ ### Resource Requirements
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+ - **CPU**: Multi-core recommended for parallel processing
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+ - **RAM**: 16GB minimum, 32GB for large papers
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+ - **GPU**: Optional for standard, required for talking-head (A6000 48GB)
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+ - **Storage**: 1-5GB per video depending on length and quality
275
+
276
+ ## Troubleshooting
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+
278
+ ### Common Issues
279
+
280
+ **1. LaTeX parsing errors**
281
+ - Ensure LaTeX source compiles successfully
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+ - Check for special packages or custom commands
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+ - Verify all referenced files are present
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+
285
+ **2. Speech synthesis problems**
286
+ - Check audio quality settings
287
+ - Verify text is properly formatted
288
+ - Test with different voice options
289
+
290
+ **3. Video rendering failures**
291
+ - Check available disk space
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+ - Verify all dependencies are installed
293
+ - Review error logs for specific issues
294
+
295
+ **4. Talking-head generation errors**
296
+ - Confirm GPU memory (48GB required)
297
+ - Check CUDA drivers are up to date
298
+ - Verify reference image quality and format
299
+
300
+ ## Integration with Other Components
301
+
302
+ Combine Paper2Video with:
303
+ - **Paper2Web**: Embed video in generated website
304
+ - **Paper2Poster**: Use matching visual style
305
+ - **AutoPR**: Create promotional clips from full video
@@ -0,0 +1,187 @@
1
+ # Paper2Web: Academic Homepage Generation
2
+
3
+ ## Overview
4
+
5
+ Paper2Web converts academic papers into interactive, explorable academic homepages. Unlike traditional approaches (direct generation, template-based, or HTML conversion), Paper2Web creates layout-aware, interactive websites through an iterative refinement process.
6
+
7
+ ## Core Capabilities
8
+
9
+ ### 1. Layout-Aware Generation
10
+ - Analyzes paper structure and content organization
11
+ - Creates responsive, multi-section layouts
12
+ - Adapts design based on paper type (research article, review, preprint, etc.)
13
+
14
+ ### 2. Interactive Elements
15
+ - Expandable sections for detailed content
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+ - Interactive figures and tables
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+ - Embedded citations and references
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+ - Navigation menu for easy browsing
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+ - Mobile-responsive design
20
+
21
+ ### 3. Content Refinement
22
+ The system uses an iterative pipeline:
23
+ 1. Initial content extraction and structuring
24
+ 2. Layout generation with visual hierarchy
25
+ 3. Interactive element integration
26
+ 4. Aesthetic refinement
27
+ 5. Quality assessment and validation
28
+
29
+ ## Usage
30
+
31
+ ### Basic Website Generation
32
+
33
+ ```bash
34
+ python pipeline_all.py \
35
+ --input-dir "path/to/papers" \
36
+ --output-dir "path/to/output" \
37
+ --model-choice 1
38
+ ```
39
+
40
+ ### Parameters
41
+
42
+ - `--input-dir`: Directory containing paper files (PDF or LaTeX)
43
+ - `--output-dir`: Directory for generated website files
44
+ - `--model-choice`: LLM model selection (1=GPT-4, 2=GPT-4.1)
45
+ - `--enable-logo-search`: Use Google Search API to find institution logos (optional)
46
+
47
+ ### Input Format Requirements
48
+
49
+ **Supported Input Formats:**
50
+ 1. **LaTeX source** (preferred for best results)
51
+ - Main file: `main.tex`
52
+ - Include all referenced figures, tables, and bibliography files
53
+ - Organize in a single directory per paper
54
+
55
+ 2. **PDF files**
56
+ - High-quality PDF with selectable text
57
+ - Embedded figures should be high resolution
58
+ - Proper section headers and structure
59
+
60
+ **Directory Structure:**
61
+ ```
62
+ input/
63
+ └── paper_name/
64
+ ├── main.tex # LaTeX source
65
+ ├── bibliography.bib # References
66
+ ├── figures/ # Figure files
67
+ │ ├── fig1.png
68
+ │ └── fig2.pdf
69
+ └── tables/ # Table files
70
+ ```
71
+
72
+ ## Output Structure
73
+
74
+ Generated websites include:
75
+
76
+ ```
77
+ output/paper_name/website/
78
+ ├── index.html # Main webpage
79
+ ├── styles.css # Styling
80
+ ├── script.js # Interactive features
81
+ ├── assets/ # Images and media
82
+ │ ├── figures/
83
+ │ └── logos/
84
+ └── data/ # Structured data (optional)
85
+ ```
86
+
87
+ ## Customization Options
88
+
89
+ ### Visual Design
90
+ The generated websites automatically include:
91
+ - Professional color schemes based on paper content
92
+ - Typography optimized for readability
93
+ - Consistent spacing and visual hierarchy
94
+ - Dark mode support (optional)
95
+
96
+ ### Content Sections
97
+ Standard sections include:
98
+ - Abstract
99
+ - Key findings/contributions
100
+ - Methodology overview
101
+ - Results and visualizations
102
+ - Discussion and implications
103
+ - References and citations
104
+ - Author information and affiliations
105
+
106
+ Additional sections are automatically added based on paper content:
107
+ - Code repositories
108
+ - Dataset links
109
+ - Supplementary materials
110
+ - Related publications
111
+
112
+ ## Quality Assessment
113
+
114
+ Paper2Web includes built-in evaluation:
115
+
116
+ ### Aesthetic Metrics
117
+ - Layout balance and spacing
118
+ - Color harmony
119
+ - Typography consistency
120
+ - Visual hierarchy effectiveness
121
+
122
+ ### Informativeness Metrics
123
+ - Content completeness
124
+ - Key finding clarity
125
+ - Method explanation adequacy
126
+ - Results presentation quality
127
+
128
+ ### Technical Metrics
129
+ - Page load time
130
+ - Mobile responsiveness
131
+ - Browser compatibility
132
+ - Accessibility compliance
133
+
134
+ ## Advanced Features
135
+
136
+ ### Logo Discovery
137
+ When enabled with Google Search API:
138
+ - Automatically finds institution logos
139
+ - Matches author affiliations
140
+ - Downloads and optimizes logo images
141
+ - Integrates into website header
142
+
143
+ ### Citation Integration
144
+ - Interactive reference list
145
+ - Hover previews for citations
146
+ - Links to DOI and external sources
147
+ - Citation count tracking (if available)
148
+
149
+ ### Figure Enhancement
150
+ - High-resolution figure rendering
151
+ - Zoom and pan functionality
152
+ - Caption and description integration
153
+ - Multi-panel figure navigation
154
+
155
+ ## Best Practices
156
+
157
+ ### Input Preparation
158
+ 1. **Use LaTeX when possible**: Provides best structure extraction
159
+ 2. **Include all assets**: Figures, tables, and bibliography files
160
+ 3. **Clean formatting**: Remove compilation artifacts and temporary files
161
+ 4. **High-quality figures**: Use vector formats (PDF, SVG) when available
162
+
163
+ ### Model Selection
164
+ - **GPT-4**: Best balance of quality and cost
165
+ - **GPT-4.1**: Latest features, higher cost
166
+ - **GPT-3.5-turbo**: Faster processing, acceptable for simple papers
167
+
168
+ ### Output Optimization
169
+ 1. Review generated content for accuracy
170
+ 2. Check that all figures render correctly
171
+ 3. Test interactive elements functionality
172
+ 4. Verify mobile responsiveness
173
+ 5. Validate external links
174
+
175
+ ## Limitations
176
+
177
+ - Complex mathematical equations may require manual review
178
+ - Multi-column layouts in PDF may affect extraction quality
179
+ - Large papers (>50 pages) may require extended processing time
180
+ - Some specialized figure types may need manual adjustment
181
+
182
+ ## Integration with Other Components
183
+
184
+ Paper2Web can be combined with:
185
+ - **Paper2Video**: Generate companion video for the website
186
+ - **Paper2Poster**: Create matching poster design
187
+ - **AutoPR**: Generate promotional content linking to website