scientific-writer 2.3.1__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- scientific_writer/.claude/WRITER.md +822 -0
- scientific_writer/.claude/settings.local.json +30 -0
- scientific_writer/.claude/skills/citation-management/SKILL.md +1046 -0
- scientific_writer/.claude/skills/citation-management/assets/bibtex_template.bib +264 -0
- scientific_writer/.claude/skills/citation-management/assets/citation_checklist.md +386 -0
- scientific_writer/.claude/skills/citation-management/references/bibtex_formatting.md +908 -0
- scientific_writer/.claude/skills/citation-management/references/citation_validation.md +794 -0
- scientific_writer/.claude/skills/citation-management/references/google_scholar_search.md +725 -0
- scientific_writer/.claude/skills/citation-management/references/metadata_extraction.md +870 -0
- scientific_writer/.claude/skills/citation-management/references/pubmed_search.md +839 -0
- scientific_writer/.claude/skills/citation-management/scripts/doi_to_bibtex.py +204 -0
- scientific_writer/.claude/skills/citation-management/scripts/extract_metadata.py +569 -0
- scientific_writer/.claude/skills/citation-management/scripts/format_bibtex.py +349 -0
- scientific_writer/.claude/skills/citation-management/scripts/search_google_scholar.py +282 -0
- scientific_writer/.claude/skills/citation-management/scripts/search_pubmed.py +398 -0
- scientific_writer/.claude/skills/citation-management/scripts/validate_citations.py +497 -0
- scientific_writer/.claude/skills/clinical-reports/IMPLEMENTATION_SUMMARY.md +641 -0
- scientific_writer/.claude/skills/clinical-reports/README.md +236 -0
- scientific_writer/.claude/skills/clinical-reports/SKILL.md +1088 -0
- scientific_writer/.claude/skills/clinical-reports/assets/case_report_template.md +352 -0
- scientific_writer/.claude/skills/clinical-reports/assets/clinical_trial_csr_template.md +353 -0
- scientific_writer/.claude/skills/clinical-reports/assets/clinical_trial_sae_template.md +359 -0
- scientific_writer/.claude/skills/clinical-reports/assets/consult_note_template.md +305 -0
- scientific_writer/.claude/skills/clinical-reports/assets/discharge_summary_template.md +453 -0
- scientific_writer/.claude/skills/clinical-reports/assets/hipaa_compliance_checklist.md +395 -0
- scientific_writer/.claude/skills/clinical-reports/assets/history_physical_template.md +305 -0
- scientific_writer/.claude/skills/clinical-reports/assets/lab_report_template.md +309 -0
- scientific_writer/.claude/skills/clinical-reports/assets/pathology_report_template.md +249 -0
- scientific_writer/.claude/skills/clinical-reports/assets/quality_checklist.md +338 -0
- scientific_writer/.claude/skills/clinical-reports/assets/radiology_report_template.md +318 -0
- scientific_writer/.claude/skills/clinical-reports/assets/soap_note_template.md +253 -0
- scientific_writer/.claude/skills/clinical-reports/references/case_report_guidelines.md +570 -0
- scientific_writer/.claude/skills/clinical-reports/references/clinical_trial_reporting.md +693 -0
- scientific_writer/.claude/skills/clinical-reports/references/data_presentation.md +530 -0
- scientific_writer/.claude/skills/clinical-reports/references/diagnostic_reports_standards.md +629 -0
- scientific_writer/.claude/skills/clinical-reports/references/medical_terminology.md +588 -0
- scientific_writer/.claude/skills/clinical-reports/references/patient_documentation.md +744 -0
- scientific_writer/.claude/skills/clinical-reports/references/peer_review_standards.md +585 -0
- scientific_writer/.claude/skills/clinical-reports/references/regulatory_compliance.md +577 -0
- scientific_writer/.claude/skills/clinical-reports/scripts/check_deidentification.py +346 -0
- scientific_writer/.claude/skills/clinical-reports/scripts/compliance_checker.py +78 -0
- scientific_writer/.claude/skills/clinical-reports/scripts/extract_clinical_data.py +102 -0
- scientific_writer/.claude/skills/clinical-reports/scripts/format_adverse_events.py +103 -0
- scientific_writer/.claude/skills/clinical-reports/scripts/generate_report_template.py +163 -0
- scientific_writer/.claude/skills/clinical-reports/scripts/terminology_validator.py +133 -0
- scientific_writer/.claude/skills/clinical-reports/scripts/validate_case_report.py +334 -0
- scientific_writer/.claude/skills/clinical-reports/scripts/validate_trial_report.py +89 -0
- scientific_writer/.claude/skills/document-skills/docx/LICENSE.txt +30 -0
- scientific_writer/.claude/skills/document-skills/docx/SKILL.md +197 -0
- scientific_writer/.claude/skills/document-skills/docx/docx-js.md +350 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/mce/mc.xsd +75 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2012.xsd +67 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2018.xsd +14 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cex-2018.xsd +20 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cid-2016.xsd +13 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-symex-2015.xsd +8 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/pack.py +159 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/unpack.py +29 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validate.py +69 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/__init__.py +15 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/base.py +951 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/docx.py +274 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/pptx.py +315 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/redlining.py +279 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml.md +610 -0
- scientific_writer/.claude/skills/document-skills/docx/scripts/__init__.py +1 -0
- scientific_writer/.claude/skills/document-skills/docx/scripts/document.py +1276 -0
- scientific_writer/.claude/skills/document-skills/docx/scripts/templates/comments.xml +3 -0
- scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsExtended.xml +3 -0
- scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsExtensible.xml +3 -0
- scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsIds.xml +3 -0
- scientific_writer/.claude/skills/document-skills/docx/scripts/templates/people.xml +3 -0
- scientific_writer/.claude/skills/document-skills/docx/scripts/utilities.py +374 -0
- scientific_writer/.claude/skills/document-skills/pdf/LICENSE.txt +30 -0
- scientific_writer/.claude/skills/document-skills/pdf/SKILL.md +294 -0
- scientific_writer/.claude/skills/document-skills/pdf/forms.md +205 -0
- scientific_writer/.claude/skills/document-skills/pdf/reference.md +612 -0
- scientific_writer/.claude/skills/document-skills/pdf/scripts/check_bounding_boxes.py +70 -0
- scientific_writer/.claude/skills/document-skills/pdf/scripts/check_bounding_boxes_test.py +226 -0
- scientific_writer/.claude/skills/document-skills/pdf/scripts/check_fillable_fields.py +12 -0
- scientific_writer/.claude/skills/document-skills/pdf/scripts/convert_pdf_to_images.py +35 -0
- scientific_writer/.claude/skills/document-skills/pdf/scripts/create_validation_image.py +41 -0
- scientific_writer/.claude/skills/document-skills/pdf/scripts/extract_form_field_info.py +152 -0
- scientific_writer/.claude/skills/document-skills/pdf/scripts/fill_fillable_fields.py +114 -0
- scientific_writer/.claude/skills/document-skills/pdf/scripts/fill_pdf_form_with_annotations.py +108 -0
- scientific_writer/.claude/skills/document-skills/pptx/LICENSE.txt +30 -0
- scientific_writer/.claude/skills/document-skills/pptx/SKILL.md +484 -0
- scientific_writer/.claude/skills/document-skills/pptx/html2pptx.md +625 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/mce/mc.xsd +75 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2012.xsd +67 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2018.xsd +14 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cex-2018.xsd +20 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cid-2016.xsd +13 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-symex-2015.xsd +8 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/pack.py +159 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/unpack.py +29 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validate.py +69 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/__init__.py +15 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/base.py +951 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/docx.py +274 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/pptx.py +315 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/redlining.py +279 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml.md +427 -0
- scientific_writer/.claude/skills/document-skills/pptx/scripts/html2pptx.js +979 -0
- scientific_writer/.claude/skills/document-skills/pptx/scripts/inventory.py +1020 -0
- scientific_writer/.claude/skills/document-skills/pptx/scripts/rearrange.py +231 -0
- scientific_writer/.claude/skills/document-skills/pptx/scripts/replace.py +385 -0
- scientific_writer/.claude/skills/document-skills/pptx/scripts/thumbnail.py +450 -0
- scientific_writer/.claude/skills/document-skills/xlsx/LICENSE.txt +30 -0
- scientific_writer/.claude/skills/document-skills/xlsx/SKILL.md +289 -0
- scientific_writer/.claude/skills/document-skills/xlsx/recalc.py +178 -0
- scientific_writer/.claude/skills/hypothesis-generation/SKILL.md +155 -0
- scientific_writer/.claude/skills/hypothesis-generation/assets/hypothesis_output_template.md +302 -0
- scientific_writer/.claude/skills/hypothesis-generation/references/experimental_design_patterns.md +327 -0
- scientific_writer/.claude/skills/hypothesis-generation/references/hypothesis_quality_criteria.md +196 -0
- scientific_writer/.claude/skills/hypothesis-generation/references/literature_search_strategies.md +505 -0
- scientific_writer/.claude/skills/latex-posters/README.md +417 -0
- scientific_writer/.claude/skills/latex-posters/SKILL.md +919 -0
- scientific_writer/.claude/skills/latex-posters/assets/baposter_template.tex +257 -0
- scientific_writer/.claude/skills/latex-posters/assets/beamerposter_template.tex +244 -0
- scientific_writer/.claude/skills/latex-posters/assets/poster_quality_checklist.md +358 -0
- scientific_writer/.claude/skills/latex-posters/assets/tikzposter_template.tex +251 -0
- scientific_writer/.claude/skills/latex-posters/references/latex_poster_packages.md +745 -0
- scientific_writer/.claude/skills/latex-posters/references/poster_content_guide.md +748 -0
- scientific_writer/.claude/skills/latex-posters/references/poster_design_principles.md +806 -0
- scientific_writer/.claude/skills/latex-posters/references/poster_layout_design.md +900 -0
- scientific_writer/.claude/skills/latex-posters/scripts/review_poster.sh +214 -0
- scientific_writer/.claude/skills/literature-review/SKILL.md +546 -0
- scientific_writer/.claude/skills/literature-review/assets/review_template.md +412 -0
- scientific_writer/.claude/skills/literature-review/references/citation_styles.md +166 -0
- scientific_writer/.claude/skills/literature-review/references/database_strategies.md +381 -0
- scientific_writer/.claude/skills/literature-review/scripts/generate_pdf.py +176 -0
- scientific_writer/.claude/skills/literature-review/scripts/search_databases.py +303 -0
- scientific_writer/.claude/skills/literature-review/scripts/verify_citations.py +222 -0
- scientific_writer/.claude/skills/markitdown/INSTALLATION_GUIDE.md +318 -0
- scientific_writer/.claude/skills/markitdown/LICENSE.txt +22 -0
- scientific_writer/.claude/skills/markitdown/OPENROUTER_INTEGRATION.md +359 -0
- scientific_writer/.claude/skills/markitdown/QUICK_REFERENCE.md +309 -0
- scientific_writer/.claude/skills/markitdown/README.md +184 -0
- scientific_writer/.claude/skills/markitdown/SKILL.md +450 -0
- scientific_writer/.claude/skills/markitdown/SKILL_SUMMARY.md +307 -0
- scientific_writer/.claude/skills/markitdown/assets/example_usage.md +463 -0
- scientific_writer/.claude/skills/markitdown/references/api_reference.md +399 -0
- scientific_writer/.claude/skills/markitdown/references/file_formats.md +542 -0
- scientific_writer/.claude/skills/markitdown/scripts/batch_convert.py +228 -0
- scientific_writer/.claude/skills/markitdown/scripts/convert_literature.py +283 -0
- scientific_writer/.claude/skills/markitdown/scripts/convert_with_ai.py +243 -0
- scientific_writer/.claude/skills/paper-2-web/SKILL.md +455 -0
- scientific_writer/.claude/skills/paper-2-web/references/installation.md +141 -0
- scientific_writer/.claude/skills/paper-2-web/references/paper2poster.md +346 -0
- scientific_writer/.claude/skills/paper-2-web/references/paper2video.md +305 -0
- scientific_writer/.claude/skills/paper-2-web/references/paper2web.md +187 -0
- scientific_writer/.claude/skills/paper-2-web/references/usage_examples.md +436 -0
- scientific_writer/.claude/skills/peer-review/SKILL.md +375 -0
- scientific_writer/.claude/skills/peer-review/references/common_issues.md +552 -0
- scientific_writer/.claude/skills/peer-review/references/reporting_standards.md +290 -0
- scientific_writer/.claude/skills/research-grants/README.md +285 -0
- scientific_writer/.claude/skills/research-grants/SKILL.md +896 -0
- scientific_writer/.claude/skills/research-grants/assets/budget_justification_template.md +453 -0
- scientific_writer/.claude/skills/research-grants/assets/nih_specific_aims_template.md +166 -0
- scientific_writer/.claude/skills/research-grants/assets/nsf_project_summary_template.md +92 -0
- scientific_writer/.claude/skills/research-grants/references/broader_impacts.md +392 -0
- scientific_writer/.claude/skills/research-grants/references/darpa_guidelines.md +636 -0
- scientific_writer/.claude/skills/research-grants/references/doe_guidelines.md +586 -0
- scientific_writer/.claude/skills/research-grants/references/nih_guidelines.md +851 -0
- scientific_writer/.claude/skills/research-grants/references/nsf_guidelines.md +570 -0
- scientific_writer/.claude/skills/research-grants/references/specific_aims_guide.md +458 -0
- scientific_writer/.claude/skills/research-lookup/README.md +116 -0
- scientific_writer/.claude/skills/research-lookup/SKILL.md +443 -0
- scientific_writer/.claude/skills/research-lookup/examples.py +174 -0
- scientific_writer/.claude/skills/research-lookup/lookup.py +93 -0
- scientific_writer/.claude/skills/research-lookup/research_lookup.py +335 -0
- scientific_writer/.claude/skills/research-lookup/scripts/research_lookup.py +261 -0
- scientific_writer/.claude/skills/scholar-evaluation/SKILL.md +254 -0
- scientific_writer/.claude/skills/scholar-evaluation/references/evaluation_framework.md +663 -0
- scientific_writer/.claude/skills/scholar-evaluation/scripts/calculate_scores.py +378 -0
- scientific_writer/.claude/skills/scientific-critical-thinking/SKILL.md +530 -0
- scientific_writer/.claude/skills/scientific-critical-thinking/references/common_biases.md +364 -0
- scientific_writer/.claude/skills/scientific-critical-thinking/references/evidence_hierarchy.md +484 -0
- scientific_writer/.claude/skills/scientific-critical-thinking/references/experimental_design.md +496 -0
- scientific_writer/.claude/skills/scientific-critical-thinking/references/logical_fallacies.md +478 -0
- scientific_writer/.claude/skills/scientific-critical-thinking/references/scientific_method.md +169 -0
- scientific_writer/.claude/skills/scientific-critical-thinking/references/statistical_pitfalls.md +506 -0
- scientific_writer/.claude/skills/scientific-schematics/SKILL.md +2035 -0
- scientific_writer/.claude/skills/scientific-schematics/assets/block_diagram_template.tex +199 -0
- scientific_writer/.claude/skills/scientific-schematics/assets/circuit_template.tex +159 -0
- scientific_writer/.claude/skills/scientific-schematics/assets/flowchart_template.tex +161 -0
- scientific_writer/.claude/skills/scientific-schematics/assets/pathway_template.tex +162 -0
- scientific_writer/.claude/skills/scientific-schematics/assets/tikz_styles.tex +422 -0
- scientific_writer/.claude/skills/scientific-schematics/references/best_practices.md +562 -0
- scientific_writer/.claude/skills/scientific-schematics/references/diagram_types.md +637 -0
- scientific_writer/.claude/skills/scientific-schematics/references/python_libraries.md +791 -0
- scientific_writer/.claude/skills/scientific-schematics/references/tikz_guide.md +734 -0
- scientific_writer/.claude/skills/scientific-schematics/scripts/circuit_generator.py +307 -0
- scientific_writer/.claude/skills/scientific-schematics/scripts/compile_tikz.py +292 -0
- scientific_writer/.claude/skills/scientific-schematics/scripts/generate_flowchart.py +281 -0
- scientific_writer/.claude/skills/scientific-schematics/scripts/pathway_diagram.py +406 -0
- scientific_writer/.claude/skills/scientific-writing/SKILL.md +443 -0
- scientific_writer/.claude/skills/scientific-writing/references/citation_styles.md +720 -0
- scientific_writer/.claude/skills/scientific-writing/references/figures_tables.md +806 -0
- scientific_writer/.claude/skills/scientific-writing/references/imrad_structure.md +658 -0
- scientific_writer/.claude/skills/scientific-writing/references/reporting_guidelines.md +748 -0
- scientific_writer/.claude/skills/scientific-writing/references/writing_principles.md +824 -0
- scientific_writer/.claude/skills/treatment-plans/README.md +488 -0
- scientific_writer/.claude/skills/treatment-plans/SKILL.md +1536 -0
- scientific_writer/.claude/skills/treatment-plans/assets/STYLING_QUICK_REFERENCE.md +185 -0
- scientific_writer/.claude/skills/treatment-plans/assets/chronic_disease_management_plan.tex +665 -0
- scientific_writer/.claude/skills/treatment-plans/assets/general_medical_treatment_plan.tex +547 -0
- scientific_writer/.claude/skills/treatment-plans/assets/medical_treatment_plan.sty +222 -0
- scientific_writer/.claude/skills/treatment-plans/assets/mental_health_treatment_plan.tex +774 -0
- scientific_writer/.claude/skills/treatment-plans/assets/one_page_treatment_plan.tex +193 -0
- scientific_writer/.claude/skills/treatment-plans/assets/pain_management_plan.tex +799 -0
- scientific_writer/.claude/skills/treatment-plans/assets/perioperative_care_plan.tex +753 -0
- scientific_writer/.claude/skills/treatment-plans/assets/quality_checklist.md +471 -0
- scientific_writer/.claude/skills/treatment-plans/assets/rehabilitation_treatment_plan.tex +756 -0
- scientific_writer/.claude/skills/treatment-plans/references/goal_setting_frameworks.md +411 -0
- scientific_writer/.claude/skills/treatment-plans/references/intervention_guidelines.md +507 -0
- scientific_writer/.claude/skills/treatment-plans/references/regulatory_compliance.md +476 -0
- scientific_writer/.claude/skills/treatment-plans/references/specialty_specific_guidelines.md +655 -0
- scientific_writer/.claude/skills/treatment-plans/references/treatment_plan_standards.md +485 -0
- scientific_writer/.claude/skills/treatment-plans/scripts/check_completeness.py +318 -0
- scientific_writer/.claude/skills/treatment-plans/scripts/generate_template.py +244 -0
- scientific_writer/.claude/skills/treatment-plans/scripts/timeline_generator.py +369 -0
- scientific_writer/.claude/skills/treatment-plans/scripts/validate_treatment_plan.py +367 -0
- scientific_writer/.claude/skills/venue-templates/SKILL.md +590 -0
- scientific_writer/.claude/skills/venue-templates/assets/grants/nih_specific_aims.tex +235 -0
- scientific_writer/.claude/skills/venue-templates/assets/grants/nsf_proposal_template.tex +375 -0
- scientific_writer/.claude/skills/venue-templates/assets/journals/nature_article.tex +171 -0
- scientific_writer/.claude/skills/venue-templates/assets/journals/neurips_article.tex +283 -0
- scientific_writer/.claude/skills/venue-templates/assets/journals/plos_one.tex +317 -0
- scientific_writer/.claude/skills/venue-templates/assets/posters/beamerposter_academic.tex +311 -0
- scientific_writer/.claude/skills/venue-templates/references/conferences_formatting.md +564 -0
- scientific_writer/.claude/skills/venue-templates/references/grants_requirements.md +787 -0
- scientific_writer/.claude/skills/venue-templates/references/journals_formatting.md +486 -0
- scientific_writer/.claude/skills/venue-templates/references/posters_guidelines.md +628 -0
- scientific_writer/.claude/skills/venue-templates/scripts/customize_template.py +206 -0
- scientific_writer/.claude/skills/venue-templates/scripts/query_template.py +260 -0
- scientific_writer/.claude/skills/venue-templates/scripts/validate_format.py +255 -0
- scientific_writer/__init__.py +43 -0
- scientific_writer/api.py +393 -0
- scientific_writer/cli.py +326 -0
- scientific_writer/core.py +275 -0
- scientific_writer/models.py +76 -0
- scientific_writer/utils.py +289 -0
- scientific_writer-2.3.1.dist-info/METADATA +272 -0
- scientific_writer-2.3.1.dist-info/RECORD +315 -0
- scientific_writer-2.3.1.dist-info/WHEEL +4 -0
- scientific_writer-2.3.1.dist-info/entry_points.txt +2 -0
- scientific_writer-2.3.1.dist-info/licenses/LICENSE +22 -0
|
@@ -0,0 +1,185 @@
|
|
|
1
|
+
# Professional Treatment Plan Styling - Quick Reference
|
|
2
|
+
|
|
3
|
+
## File Location
|
|
4
|
+
`medical_treatment_plan.sty` - Available in the assets directory
|
|
5
|
+
|
|
6
|
+
## Quick Start
|
|
7
|
+
|
|
8
|
+
```latex
|
|
9
|
+
% !TEX program = xelatex
|
|
10
|
+
\documentclass[11pt,letterpaper]{article}
|
|
11
|
+
\usepackage{medical_treatment_plan}
|
|
12
|
+
\usepackage{natbib}
|
|
13
|
+
|
|
14
|
+
\begin{document}
|
|
15
|
+
\maketitle
|
|
16
|
+
% Your content
|
|
17
|
+
\end{document}
|
|
18
|
+
```
|
|
19
|
+
|
|
20
|
+
## Custom Box Environments
|
|
21
|
+
|
|
22
|
+
### 1. Info Box (Blue) - General Information
|
|
23
|
+
```latex
|
|
24
|
+
\begin{infobox}[Title]
|
|
25
|
+
Content
|
|
26
|
+
\end{infobox}
|
|
27
|
+
```
|
|
28
|
+
**Use for:** Clinical assessments, monitoring schedules, titration protocols
|
|
29
|
+
|
|
30
|
+
### 2. Warning Box (Yellow/Red) - Critical Alerts
|
|
31
|
+
```latex
|
|
32
|
+
\begin{warningbox}[Title]
|
|
33
|
+
Critical information
|
|
34
|
+
\end{warningbox}
|
|
35
|
+
```
|
|
36
|
+
**Use for:** Safety protocols, decision points, contraindications
|
|
37
|
+
|
|
38
|
+
### 3. Goal Box (Green) - Treatment Goals
|
|
39
|
+
```latex
|
|
40
|
+
\begin{goalbox}[Title]
|
|
41
|
+
Goals and targets
|
|
42
|
+
\end{goalbox}
|
|
43
|
+
```
|
|
44
|
+
**Use for:** SMART goals, target outcomes, success metrics
|
|
45
|
+
|
|
46
|
+
### 4. Key Points Box (Light Blue) - Highlights
|
|
47
|
+
```latex
|
|
48
|
+
\begin{keybox}[Title]
|
|
49
|
+
Important highlights
|
|
50
|
+
\end{keybox}
|
|
51
|
+
```
|
|
52
|
+
**Use for:** Executive summaries, key takeaways, essential recommendations
|
|
53
|
+
|
|
54
|
+
### 5. Emergency Box (Red) - Emergency Info
|
|
55
|
+
```latex
|
|
56
|
+
\begin{emergencybox}
|
|
57
|
+
Emergency contacts
|
|
58
|
+
\end{emergencybox}
|
|
59
|
+
```
|
|
60
|
+
**Use for:** Emergency contacts, urgent protocols
|
|
61
|
+
|
|
62
|
+
### 6. Patient Info Box (White/Blue) - Demographics
|
|
63
|
+
```latex
|
|
64
|
+
\begin{patientinfo}
|
|
65
|
+
Patient information
|
|
66
|
+
\end{patientinfo}
|
|
67
|
+
```
|
|
68
|
+
**Use for:** Patient demographics and baseline data
|
|
69
|
+
|
|
70
|
+
## Professional Tables
|
|
71
|
+
|
|
72
|
+
```latex
|
|
73
|
+
\begin{medtable}{Caption}
|
|
74
|
+
\begin{tabular}{|l|l|l|}
|
|
75
|
+
\hline
|
|
76
|
+
\tableheadercolor
|
|
77
|
+
\textcolor{white}{\textbf{Header 1}} & \textcolor{white}{\textbf{Header 2}} \\
|
|
78
|
+
\hline
|
|
79
|
+
Data row 1 \\
|
|
80
|
+
\hline
|
|
81
|
+
\tablerowcolor % Alternating gray
|
|
82
|
+
Data row 2 \\
|
|
83
|
+
\hline
|
|
84
|
+
\end{tabular}
|
|
85
|
+
\caption{Table caption}
|
|
86
|
+
\end{medtable}
|
|
87
|
+
```
|
|
88
|
+
|
|
89
|
+
## Color Scheme
|
|
90
|
+
|
|
91
|
+
- **Primary Blue** (0, 102, 153): Headers, titles
|
|
92
|
+
- **Secondary Blue** (102, 178, 204): Light backgrounds
|
|
93
|
+
- **Accent Blue** (0, 153, 204): Links, highlights
|
|
94
|
+
- **Success Green** (0, 153, 76): Goals
|
|
95
|
+
- **Warning Red** (204, 0, 0): Warnings
|
|
96
|
+
|
|
97
|
+
## Compilation
|
|
98
|
+
|
|
99
|
+
```bash
|
|
100
|
+
xelatex document.tex
|
|
101
|
+
bibtex document
|
|
102
|
+
xelatex document.tex
|
|
103
|
+
xelatex document.tex
|
|
104
|
+
```
|
|
105
|
+
|
|
106
|
+
## Best Practices
|
|
107
|
+
|
|
108
|
+
1. **Match box type to purpose:** Green for goals, red/yellow for warnings
|
|
109
|
+
2. **Don't overuse boxes:** Reserve for important information only
|
|
110
|
+
3. **Maintain color consistency:** Stick to the defined scheme
|
|
111
|
+
4. **Use white space:** Add `\vspace{0.5cm}` between major sections
|
|
112
|
+
5. **Table alternating rows:** Use `\tablerowcolor` for readability
|
|
113
|
+
|
|
114
|
+
## Installation
|
|
115
|
+
|
|
116
|
+
**Option 1:** Copy `assets/medical_treatment_plan.sty` to your document directory
|
|
117
|
+
|
|
118
|
+
**Option 2:** Install to user TeX directory
|
|
119
|
+
```bash
|
|
120
|
+
mkdir -p ~/texmf/tex/latex/medical_treatment_plan
|
|
121
|
+
cp assets/medical_treatment_plan.sty ~/texmf/tex/latex/medical_treatment_plan/
|
|
122
|
+
texhash ~/texmf
|
|
123
|
+
```
|
|
124
|
+
|
|
125
|
+
## Required Packages
|
|
126
|
+
All automatically loaded by the style:
|
|
127
|
+
- tcolorbox, tikz, xcolor
|
|
128
|
+
- fancyhdr, titlesec, enumitem
|
|
129
|
+
- booktabs, longtable, array, colortbl
|
|
130
|
+
- hyperref, natbib, fontspec
|
|
131
|
+
|
|
132
|
+
## Example Structure
|
|
133
|
+
|
|
134
|
+
```latex
|
|
135
|
+
\maketitle
|
|
136
|
+
|
|
137
|
+
\section*{Patient Information}
|
|
138
|
+
\begin{patientinfo}
|
|
139
|
+
Demographics
|
|
140
|
+
\end{patientinfo}
|
|
141
|
+
|
|
142
|
+
\section{Executive Summary}
|
|
143
|
+
\begin{keybox}[Plan Overview]
|
|
144
|
+
Key highlights
|
|
145
|
+
\end{keybox}
|
|
146
|
+
|
|
147
|
+
\section{Treatment Goals}
|
|
148
|
+
\begin{goalbox}[SMART Goals]
|
|
149
|
+
Goals list
|
|
150
|
+
\end{goalbox}
|
|
151
|
+
|
|
152
|
+
\section{Medication Plan}
|
|
153
|
+
\begin{infobox}[Dosing]
|
|
154
|
+
Instructions
|
|
155
|
+
\end{infobox}
|
|
156
|
+
|
|
157
|
+
\begin{warningbox}[Safety]
|
|
158
|
+
Warnings
|
|
159
|
+
\end{warningbox}
|
|
160
|
+
|
|
161
|
+
\section{Emergency}
|
|
162
|
+
\begin{emergencybox}
|
|
163
|
+
Contacts
|
|
164
|
+
\end{emergencybox}
|
|
165
|
+
```
|
|
166
|
+
|
|
167
|
+
## Troubleshooting
|
|
168
|
+
|
|
169
|
+
**Missing packages:**
|
|
170
|
+
```bash
|
|
171
|
+
sudo tlmgr install tcolorbox tikz pgf
|
|
172
|
+
```
|
|
173
|
+
|
|
174
|
+
**Special characters not showing:**
|
|
175
|
+
- Use XeLaTeX instead of PDFLaTeX
|
|
176
|
+
- Or use LaTeX commands: `$\checkmark$`, `$\geq$`
|
|
177
|
+
|
|
178
|
+
**Header warnings:**
|
|
179
|
+
- Already set to 22pt in style file
|
|
180
|
+
- Adjust if needed
|
|
181
|
+
|
|
182
|
+
---
|
|
183
|
+
|
|
184
|
+
For complete documentation, see the "Professional Document Styling" section in SKILL.md
|
|
185
|
+
|