scientific-writer 2.0.0__tar.gz → 2.1.0__tar.gz

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  1. scientific_writer-2.1.0/.claude/settings.local.json +16 -0
  2. scientific_writer-2.1.0/.claude/skills/citation-management/SKILL.md +1046 -0
  3. scientific_writer-2.1.0/.claude/skills/citation-management/assets/bibtex_template.bib +264 -0
  4. scientific_writer-2.1.0/.claude/skills/citation-management/assets/citation_checklist.md +386 -0
  5. scientific_writer-2.1.0/.claude/skills/citation-management/references/bibtex_formatting.md +908 -0
  6. scientific_writer-2.1.0/.claude/skills/citation-management/references/citation_validation.md +794 -0
  7. scientific_writer-2.1.0/.claude/skills/citation-management/references/google_scholar_search.md +725 -0
  8. scientific_writer-2.1.0/.claude/skills/citation-management/references/metadata_extraction.md +870 -0
  9. scientific_writer-2.1.0/.claude/skills/citation-management/references/pubmed_search.md +839 -0
  10. scientific_writer-2.1.0/.claude/skills/citation-management/scripts/doi_to_bibtex.py +204 -0
  11. scientific_writer-2.1.0/.claude/skills/citation-management/scripts/extract_metadata.py +569 -0
  12. scientific_writer-2.1.0/.claude/skills/citation-management/scripts/format_bibtex.py +349 -0
  13. scientific_writer-2.1.0/.claude/skills/citation-management/scripts/search_google_scholar.py +282 -0
  14. scientific_writer-2.1.0/.claude/skills/citation-management/scripts/search_pubmed.py +398 -0
  15. scientific_writer-2.1.0/.claude/skills/citation-management/scripts/validate_citations.py +497 -0
  16. scientific_writer-2.1.0/.claude/skills/research-grants/README.md +285 -0
  17. scientific_writer-2.1.0/.claude/skills/research-grants/SKILL.md +896 -0
  18. scientific_writer-2.1.0/.claude/skills/research-grants/assets/budget_justification_template.md +453 -0
  19. scientific_writer-2.1.0/.claude/skills/research-grants/assets/nih_specific_aims_template.md +166 -0
  20. scientific_writer-2.1.0/.claude/skills/research-grants/assets/nsf_project_summary_template.md +92 -0
  21. scientific_writer-2.1.0/.claude/skills/research-grants/references/broader_impacts.md +392 -0
  22. scientific_writer-2.1.0/.claude/skills/research-grants/references/darpa_guidelines.md +636 -0
  23. scientific_writer-2.1.0/.claude/skills/research-grants/references/doe_guidelines.md +586 -0
  24. scientific_writer-2.1.0/.claude/skills/research-grants/references/nih_guidelines.md +851 -0
  25. scientific_writer-2.1.0/.claude/skills/research-grants/references/nsf_guidelines.md +570 -0
  26. scientific_writer-2.1.0/.claude/skills/research-grants/references/specific_aims_guide.md +458 -0
  27. scientific_writer-2.1.0/.claude/skills/scholar-evaluation/SKILL.md +254 -0
  28. scientific_writer-2.1.0/.claude/skills/scholar-evaluation/references/evaluation_framework.md +663 -0
  29. scientific_writer-2.1.0/.claude/skills/scholar-evaluation/scripts/calculate_scores.py +378 -0
  30. scientific_writer-2.1.0/.claude/skills/scientific-schematics/SKILL.md +2035 -0
  31. scientific_writer-2.1.0/.claude/skills/scientific-schematics/assets/block_diagram_template.tex +199 -0
  32. scientific_writer-2.1.0/.claude/skills/scientific-schematics/assets/circuit_template.tex +159 -0
  33. scientific_writer-2.1.0/.claude/skills/scientific-schematics/assets/flowchart_template.tex +161 -0
  34. scientific_writer-2.1.0/.claude/skills/scientific-schematics/assets/pathway_template.tex +162 -0
  35. scientific_writer-2.1.0/.claude/skills/scientific-schematics/assets/tikz_styles.tex +422 -0
  36. scientific_writer-2.1.0/.claude/skills/scientific-schematics/references/best_practices.md +562 -0
  37. scientific_writer-2.1.0/.claude/skills/scientific-schematics/references/diagram_types.md +637 -0
  38. scientific_writer-2.1.0/.claude/skills/scientific-schematics/references/python_libraries.md +791 -0
  39. scientific_writer-2.1.0/.claude/skills/scientific-schematics/references/tikz_guide.md +734 -0
  40. scientific_writer-2.1.0/.claude/skills/scientific-schematics/scripts/circuit_generator.py +307 -0
  41. scientific_writer-2.1.0/.claude/skills/scientific-schematics/scripts/compile_tikz.py +292 -0
  42. scientific_writer-2.1.0/.claude/skills/scientific-schematics/scripts/generate_flowchart.py +281 -0
  43. scientific_writer-2.1.0/.claude/skills/scientific-schematics/scripts/pathway_diagram.py +406 -0
  44. scientific_writer-2.1.0/.claude/skills/venue-templates/SKILL.md +590 -0
  45. scientific_writer-2.1.0/.claude/skills/venue-templates/assets/grants/nih_specific_aims.tex +235 -0
  46. scientific_writer-2.1.0/.claude/skills/venue-templates/assets/grants/nsf_proposal_template.tex +375 -0
  47. scientific_writer-2.1.0/.claude/skills/venue-templates/assets/journals/nature_article.tex +171 -0
  48. scientific_writer-2.1.0/.claude/skills/venue-templates/assets/journals/neurips_article.tex +283 -0
  49. scientific_writer-2.1.0/.claude/skills/venue-templates/assets/journals/plos_one.tex +317 -0
  50. scientific_writer-2.1.0/.claude/skills/venue-templates/assets/posters/beamerposter_academic.tex +311 -0
  51. scientific_writer-2.1.0/.claude/skills/venue-templates/references/conferences_formatting.md +564 -0
  52. scientific_writer-2.1.0/.claude/skills/venue-templates/references/grants_requirements.md +787 -0
  53. scientific_writer-2.1.0/.claude/skills/venue-templates/references/journals_formatting.md +486 -0
  54. scientific_writer-2.1.0/.claude/skills/venue-templates/references/posters_guidelines.md +628 -0
  55. scientific_writer-2.1.0/.claude/skills/venue-templates/scripts/customize_template.py +206 -0
  56. scientific_writer-2.1.0/.claude/skills/venue-templates/scripts/query_template.py +260 -0
  57. scientific_writer-2.1.0/.claude/skills/venue-templates/scripts/validate_format.py +255 -0
  58. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/CHANGELOG.md +81 -0
  59. scientific_writer-2.1.0/CLAUDE.md +748 -0
  60. scientific_writer-2.1.0/PKG-INFO +268 -0
  61. scientific_writer-2.1.0/README.md +256 -0
  62. {scientific_writer-2.0.0/Docs → scientific_writer-2.1.0/docs}/API.md +217 -5
  63. scientific_writer-2.1.0/docs/FEATURES.md +514 -0
  64. scientific_writer-2.1.0/docs/README.md +165 -0
  65. scientific_writer-2.1.0/docs/SKILLS.md +551 -0
  66. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/pyproject.toml +1 -1
  67. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/scientific_writer/__init__.py +1 -1
  68. scientific_writer-2.0.0/CLAUDE.md +0 -1331
  69. scientific_writer-2.0.0/Docs/SKILLS.md +0 -284
  70. scientific_writer-2.0.0/PKG-INFO +0 -98
  71. scientific_writer-2.0.0/README.md +0 -86
  72. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/LICENSE.txt +0 -0
  73. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/SKILL.md +0 -0
  74. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/docx-js.md +0 -0
  75. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +0 -0
  76. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +0 -0
  77. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +0 -0
  78. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +0 -0
  79. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +0 -0
  80. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +0 -0
  81. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +0 -0
  82. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +0 -0
  83. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +0 -0
  84. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +0 -0
  85. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +0 -0
  86. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +0 -0
  87. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +0 -0
  88. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +0 -0
  89. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +0 -0
  90. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +0 -0
  91. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +0 -0
  92. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd +0 -0
  93. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +0 -0
  94. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +0 -0
  95. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +0 -0
  96. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +0 -0
  97. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +0 -0
  98. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +0 -0
  99. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +0 -0
  100. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +0 -0
  101. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +0 -0
  102. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +0 -0
  103. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +0 -0
  104. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +0 -0
  105. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +0 -0
  106. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/mce/mc.xsd +0 -0
  107. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2010.xsd +0 -0
  108. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2012.xsd +0 -0
  109. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2018.xsd +0 -0
  110. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cex-2018.xsd +0 -0
  111. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cid-2016.xsd +0 -0
  112. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +0 -0
  113. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-symex-2015.xsd +0 -0
  114. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/scripts/pack.py +0 -0
  115. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/scripts/unpack.py +0 -0
  116. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/scripts/validate.py +0 -0
  117. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/scripts/validation/__init__.py +0 -0
  118. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/scripts/validation/base.py +0 -0
  119. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/scripts/validation/docx.py +0 -0
  120. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/scripts/validation/pptx.py +0 -0
  121. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml/scripts/validation/redlining.py +0 -0
  122. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/ooxml.md +0 -0
  123. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/scripts/__init__.py +0 -0
  124. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/scripts/document.py +0 -0
  125. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/scripts/templates/comments.xml +0 -0
  126. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/scripts/templates/commentsExtended.xml +0 -0
  127. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/scripts/templates/commentsExtensible.xml +0 -0
  128. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/scripts/templates/commentsIds.xml +0 -0
  129. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/scripts/templates/people.xml +0 -0
  130. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/docx/scripts/utilities.py +0 -0
  131. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pdf/LICENSE.txt +0 -0
  132. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pdf/SKILL.md +0 -0
  133. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pdf/forms.md +0 -0
  134. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pdf/reference.md +0 -0
  135. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pdf/scripts/check_bounding_boxes.py +0 -0
  136. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pdf/scripts/check_bounding_boxes_test.py +0 -0
  137. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pdf/scripts/check_fillable_fields.py +0 -0
  138. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pdf/scripts/convert_pdf_to_images.py +0 -0
  139. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pdf/scripts/create_validation_image.py +0 -0
  140. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pdf/scripts/extract_form_field_info.py +0 -0
  141. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pdf/scripts/fill_fillable_fields.py +0 -0
  142. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pdf/scripts/fill_pdf_form_with_annotations.py +0 -0
  143. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/LICENSE.txt +0 -0
  144. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/SKILL.md +0 -0
  145. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/html2pptx.md +0 -0
  146. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +0 -0
  147. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +0 -0
  148. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +0 -0
  149. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +0 -0
  150. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +0 -0
  151. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +0 -0
  152. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +0 -0
  153. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +0 -0
  154. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +0 -0
  155. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +0 -0
  156. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +0 -0
  157. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +0 -0
  158. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +0 -0
  159. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +0 -0
  160. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +0 -0
  161. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +0 -0
  162. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +0 -0
  163. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd +0 -0
  164. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +0 -0
  165. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +0 -0
  166. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +0 -0
  167. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +0 -0
  168. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +0 -0
  169. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +0 -0
  170. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +0 -0
  171. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +0 -0
  172. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +0 -0
  173. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +0 -0
  174. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +0 -0
  175. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +0 -0
  176. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +0 -0
  177. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/mce/mc.xsd +0 -0
  178. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2010.xsd +0 -0
  179. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2012.xsd +0 -0
  180. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2018.xsd +0 -0
  181. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cex-2018.xsd +0 -0
  182. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cid-2016.xsd +0 -0
  183. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +0 -0
  184. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-symex-2015.xsd +0 -0
  185. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/scripts/pack.py +0 -0
  186. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/scripts/unpack.py +0 -0
  187. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/scripts/validate.py +0 -0
  188. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/scripts/validation/__init__.py +0 -0
  189. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/scripts/validation/base.py +0 -0
  190. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/scripts/validation/docx.py +0 -0
  191. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/scripts/validation/pptx.py +0 -0
  192. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml/scripts/validation/redlining.py +0 -0
  193. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/ooxml.md +0 -0
  194. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/scripts/html2pptx.js +0 -0
  195. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/scripts/inventory.py +0 -0
  196. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/scripts/rearrange.py +0 -0
  197. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/scripts/replace.py +0 -0
  198. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/pptx/scripts/thumbnail.py +0 -0
  199. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/xlsx/LICENSE.txt +0 -0
  200. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/xlsx/SKILL.md +0 -0
  201. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/document-skills/xlsx/recalc.py +0 -0
  202. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/hypothesis-generation/SKILL.md +0 -0
  203. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/hypothesis-generation/assets/hypothesis_output_template.md +0 -0
  204. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/hypothesis-generation/references/experimental_design_patterns.md +0 -0
  205. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/hypothesis-generation/references/hypothesis_quality_criteria.md +0 -0
  206. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/hypothesis-generation/references/literature_search_strategies.md +0 -0
  207. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/latex-posters/README.md +0 -0
  208. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/latex-posters/SKILL.md +0 -0
  209. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/latex-posters/assets/baposter_template.tex +0 -0
  210. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/latex-posters/assets/beamerposter_template.tex +0 -0
  211. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/latex-posters/assets/poster_quality_checklist.md +0 -0
  212. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/latex-posters/assets/tikzposter_template.tex +0 -0
  213. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/latex-posters/references/latex_poster_packages.md +0 -0
  214. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/latex-posters/references/poster_content_guide.md +0 -0
  215. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/latex-posters/references/poster_design_principles.md +0 -0
  216. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/latex-posters/references/poster_layout_design.md +0 -0
  217. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/latex-posters/scripts/review_poster.sh +0 -0
  218. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/literature-review/SKILL.md +0 -0
  219. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/literature-review/assets/review_template.md +0 -0
  220. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/literature-review/references/citation_styles.md +0 -0
  221. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/literature-review/references/database_strategies.md +0 -0
  222. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/literature-review/scripts/generate_pdf.py +0 -0
  223. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/literature-review/scripts/search_databases.py +0 -0
  224. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/literature-review/scripts/verify_citations.py +0 -0
  225. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/markitdown/INSTALLATION_GUIDE.md +0 -0
  226. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/markitdown/LICENSE.txt +0 -0
  227. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/markitdown/OPENROUTER_INTEGRATION.md +0 -0
  228. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/markitdown/QUICK_REFERENCE.md +0 -0
  229. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/markitdown/README.md +0 -0
  230. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/markitdown/SKILL.md +0 -0
  231. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/markitdown/SKILL_SUMMARY.md +0 -0
  232. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/markitdown/assets/example_usage.md +0 -0
  233. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/markitdown/references/api_reference.md +0 -0
  234. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/markitdown/references/file_formats.md +0 -0
  235. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/markitdown/scripts/batch_convert.py +0 -0
  236. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/markitdown/scripts/convert_literature.py +0 -0
  237. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/markitdown/scripts/convert_with_ai.py +0 -0
  238. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/paper-2-web/SKILL.md +0 -0
  239. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/paper-2-web/references/installation.md +0 -0
  240. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/paper-2-web/references/paper2poster.md +0 -0
  241. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/paper-2-web/references/paper2video.md +0 -0
  242. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/paper-2-web/references/paper2web.md +0 -0
  243. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/paper-2-web/references/usage_examples.md +0 -0
  244. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/peer-review/SKILL.md +0 -0
  245. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/peer-review/references/common_issues.md +0 -0
  246. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/peer-review/references/reporting_standards.md +0 -0
  247. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/research-lookup/README.md +0 -0
  248. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/research-lookup/SKILL.md +0 -0
  249. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/research-lookup/examples.py +0 -0
  250. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/research-lookup/lookup.py +0 -0
  251. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/research-lookup/research_lookup.py +0 -0
  252. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/research-lookup/scripts/research_lookup.py +0 -0
  253. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/scientific-critical-thinking/SKILL.md +0 -0
  254. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/scientific-critical-thinking/references/common_biases.md +0 -0
  255. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/scientific-critical-thinking/references/evidence_hierarchy.md +0 -0
  256. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/scientific-critical-thinking/references/experimental_design.md +0 -0
  257. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/scientific-critical-thinking/references/logical_fallacies.md +0 -0
  258. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/scientific-critical-thinking/references/scientific_method.md +0 -0
  259. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/scientific-critical-thinking/references/statistical_pitfalls.md +0 -0
  260. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/scientific-writing/SKILL.md +0 -0
  261. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/scientific-writing/references/citation_styles.md +0 -0
  262. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/scientific-writing/references/figures_tables.md +0 -0
  263. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/scientific-writing/references/imrad_structure.md +0 -0
  264. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/scientific-writing/references/reporting_guidelines.md +0 -0
  265. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.claude/skills/scientific-writing/references/writing_principles.md +0 -0
  266. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.env.example +0 -0
  267. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/.gitignore +0 -0
  268. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/LICENSE +0 -0
  269. {scientific_writer-2.0.0/Docs → scientific_writer-2.1.0/docs}/DEVELOPMENT.md +0 -0
  270. {scientific_writer-2.0.0/Docs → scientific_writer-2.1.0/docs}/RELEASING.md +0 -0
  271. {scientific_writer-2.0.0/Docs → scientific_writer-2.1.0/docs}/TROUBLESHOOTING.md +0 -0
  272. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/example_api_usage.py +0 -0
  273. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/scientific_writer/api.py +0 -0
  274. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/scientific_writer/cli.py +0 -0
  275. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/scientific_writer/core.py +0 -0
  276. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/scientific_writer/models.py +0 -0
  277. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/scientific_writer/utils.py +0 -0
  278. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/scripts/README.md +0 -0
  279. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/scripts/bump_version.py +0 -0
  280. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/scripts/publish.py +0 -0
  281. {scientific_writer-2.0.0 → scientific_writer-2.1.0}/scripts/verify_package.py +0 -0
scientific_writer-2.1.0/.claude/settings.local.json ADDED
@@ -0,0 +1,16 @@
1
+ {
2
+ "permissions": {
3
+ "allow": [
4
+ "Bash(mkdir:*)",
5
+ "Skill(research-lookup)",
6
+ "Bash(python research_lookup.py:*)",
7
+ "WebSearch",
8
+ "Bash(pdflatex:*)",
9
+ "Bash(bibtex:*)",
10
+ "Skill(peer-review)",
11
+ "Skill(research-grants)"
12
+ ],
13
+ "deny": [],
14
+ "ask": []
15
+ }
16
+ }