scientific-writer 2.1.1__py3-none-any.whl → 2.2.2__py3-none-any.whl
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- 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 +483 -0
- scientific_writer/.claude/skills/treatment-plans/SKILL.md +817 -0
- scientific_writer/.claude/skills/treatment-plans/assets/chronic_disease_management_plan.tex +636 -0
- scientific_writer/.claude/skills/treatment-plans/assets/general_medical_treatment_plan.tex +616 -0
- scientific_writer/.claude/skills/treatment-plans/assets/mental_health_treatment_plan.tex +745 -0
- scientific_writer/.claude/skills/treatment-plans/assets/pain_management_plan.tex +770 -0
- scientific_writer/.claude/skills/treatment-plans/assets/perioperative_care_plan.tex +724 -0
- scientific_writer/.claude/skills/treatment-plans/assets/quality_checklist.md +471 -0
- scientific_writer/.claude/skills/treatment-plans/assets/rehabilitation_treatment_plan.tex +727 -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 +607 -0
- scientific_writer/.claude/skills/treatment-plans/references/treatment_plan_standards.md +456 -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/CLAUDE.md +748 -0
- scientific_writer/__init__.py +2 -2
- scientific_writer/api.py +14 -7
- scientific_writer/cli.py +12 -7
- scientific_writer/core.py +27 -5
- {scientific_writer-2.1.1.dist-info → scientific_writer-2.2.2.dist-info}/METADATA +5 -1
- scientific_writer-2.2.2.dist-info/RECORD +312 -0
- scientific_writer-2.1.1.dist-info/RECORD +0 -11
- {scientific_writer-2.1.1.dist-info → scientific_writer-2.2.2.dist-info}/WHEEL +0 -0
- {scientific_writer-2.1.1.dist-info → scientific_writer-2.2.2.dist-info}/entry_points.txt +0 -0
- {scientific_writer-2.1.1.dist-info → scientific_writer-2.2.2.dist-info}/licenses/LICENSE +0 -0
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#!/bin/bash
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# Poster PDF Quality Check Script
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# Usage: ./review_poster.sh poster.pdf
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# Colors for output
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RED='\033[0;31m'
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GREEN='\033[0;32m'
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YELLOW='\033[1;33m'
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BLUE='\033[0;34m'
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NC='\033[0m' # No Color
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# Check if file argument provided
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if [ $# -eq 0 ]; then
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echo -e "${RED}Error: No file specified${NC}"
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echo "Usage: $0 <poster.pdf>"
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exit 1
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fi
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POSTER_FILE="$1"
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# Check if file exists
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if [ ! -f "$POSTER_FILE" ]; then
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echo -e "${RED}Error: File '$POSTER_FILE' not found${NC}"
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exit 1
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fi
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echo -e "${BLUE}═══════════════════════════════════════════════${NC}"
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echo -e "${BLUE} Poster PDF Quality Check${NC}"
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echo -e "${BLUE}═══════════════════════════════════════════════${NC}"
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echo ""
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echo -e "${GREEN}File:${NC} $POSTER_FILE"
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echo ""
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# Function to check if command exists
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command_exists() {
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command -v "$1" >/dev/null 2>&1
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}
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# 1. Page Size Check
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echo -e "${YELLOW}[1] Page Dimensions:${NC}"
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if command_exists pdfinfo; then
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PAGE_SIZE=$(pdfinfo "$POSTER_FILE" 2>/dev/null | grep "Page size")
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if [ -n "$PAGE_SIZE" ]; then
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echo " $PAGE_SIZE"
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# Extract dimensions and check common sizes
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WIDTH=$(echo "$PAGE_SIZE" | awk '{print $3}')
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HEIGHT=$(echo "$PAGE_SIZE" | awk '{print $5}')
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# Check against common poster sizes (approximate)
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if [ "$WIDTH" = "2384" ] && [ "$HEIGHT" = "3370" ]; then
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echo -e " ${GREEN}✓ Detected: A0 Portrait${NC}"
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elif [ "$WIDTH" = "3370" ] && [ "$HEIGHT" = "2384" ]; then
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echo -e " ${GREEN}✓ Detected: A0 Landscape${NC}"
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elif [ "$WIDTH" = "1684" ] && [ "$HEIGHT" = "2384" ]; then
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echo -e " ${GREEN}✓ Detected: A1 Portrait${NC}"
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elif [ "$WIDTH" = "2592" ] && [ "$HEIGHT" = "3456" ]; then
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echo -e " ${GREEN}✓ Detected: 36×48 inches Portrait${NC}"
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else
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echo -e " ${YELLOW}⚠ Non-standard size detected${NC}"
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fi
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else
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echo -e " ${RED}✗ Could not extract page size${NC}"
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fi
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else
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echo -e " ${YELLOW}⚠ pdfinfo not installed (install: brew install poppler or apt-get install poppler-utils)${NC}"
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fi
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echo ""
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# 2. Page Count
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echo -e "${YELLOW}[2] Page Count:${NC}"
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if command_exists pdfinfo; then
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PAGE_COUNT=$(pdfinfo "$POSTER_FILE" 2>/dev/null | grep "Pages" | awk '{print $2}')
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if [ "$PAGE_COUNT" = "1" ]; then
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echo -e " ${GREEN}✓ Single page (correct for poster)${NC}"
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else
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echo -e " ${RED}✗ Multiple pages detected: $PAGE_COUNT${NC}"
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echo -e " ${YELLOW} Posters should be single page${NC}"
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fi
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else
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echo -e " ${YELLOW}⚠ pdfinfo not installed${NC}"
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fi
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echo ""
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# 3. File Size
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echo -e "${YELLOW}[3] File Size:${NC}"
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if command_exists ls; then
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FILE_SIZE=$(ls -lh "$POSTER_FILE" | awk '{print $5}')
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FILE_SIZE_BYTES=$(ls -l "$POSTER_FILE" | awk '{print $5}')
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echo " Size: $FILE_SIZE"
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# Check if file is too large for email
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if [ "$FILE_SIZE_BYTES" -gt 52428800 ]; then # 50MB
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echo -e " ${YELLOW}⚠ Large file (>50MB) - may need compression for email${NC}"
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echo -e " ${BLUE} Compress with: gs -sDEVICE=pdfwrite -dPDFSETTINGS=/printer -dNOPAUSE -dQUIET -dBATCH -sOutputFile=compressed.pdf $POSTER_FILE${NC}"
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elif [ "$FILE_SIZE_BYTES" -lt 1048576 ]; then # 1MB
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echo -e " ${YELLOW}⚠ Small file - check image quality${NC}"
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else
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echo -e " ${GREEN}✓ Reasonable file size${NC}"
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fi
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fi
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echo ""
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# 4. Font Embedding Check
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echo " Checking first 20 fonts..."
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FONT_OUTPUT=$(pdffonts "$POSTER_FILE" 2>/dev/null | head -21)
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echo "$FONT_OUTPUT" | tail -20 | while IFS= read -r line; do
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echo " $line"
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done
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# Check for non-embedded fonts
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echo -e " ${RED}✗ Some fonts are NOT embedded (printing may fail)${NC}"
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echo -e " ${BLUE} Fix: Recompile with 'pdflatex -dEmbedAllFonts=true poster.tex'${NC}"
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else
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echo -e " ${GREEN}✓ All fonts appear to be embedded${NC}"
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fi
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else
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echo -e " ${YELLOW}⚠ pdffonts not installed (install: brew install poppler or apt-get install poppler-utils)${NC}"
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fi
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echo ""
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# 5. Image Quality Check
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echo -e "${YELLOW}[5] Image Quality:${NC}"
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if command_exists pdfimages; then
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IMAGE_COUNT=$(pdfimages -list "$POSTER_FILE" 2>/dev/null | tail -n +3 | wc -l | tr -d ' ')
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echo " Found $IMAGE_COUNT image(s)"
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echo " Image details:"
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echo -e " ${BLUE} Verify images are at least 300 DPI for printing${NC}"
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echo -e " ${BLUE} Formula: DPI = pixels / (inches in poster)${NC}"
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else
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fi
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else
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echo -e " ${YELLOW}⚠ pdfimages not installed (install: brew install poppler or apt-get install poppler-utils)${NC}"
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fi
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echo ""
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# 6. Manual Checks Required
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echo ""
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echo -e "${BLUE}Layout and Spacing:${NC}"
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echo " [ ] Content fills entire page (no large white margins)"
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echo " [ ] Consistent spacing between columns"
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echo " [ ] Consistent spacing between blocks/sections"
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echo " [ ] All elements aligned properly"
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echo " [ ] No overlapping text or figures"
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echo -e "${BLUE}Typography:${NC}"
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echo " [ ] Title visible and large (72pt+)"
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echo " [ ] Section headers readable (48-72pt)"
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echo " [ ] Body text readable (24-36pt minimum)"
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echo " [ ] No text cutoff or running off edges"
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echo " [ ] Consistent font usage"
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echo -e "${BLUE}Visual Elements:${NC}"
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echo " [ ] All figures display correctly"
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echo " [ ] No pixelated or blurry images"
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echo " [ ] Figure captions present and readable"
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echo " [ ] Colors render as expected"
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echo " [ ] Logos display clearly"
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echo " [ ] All sections present (Intro, Methods, Results, Conclusions)"
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echo " [ ] References included"
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echo " [ ] Contact information visible"
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# 7. Recommended Tests
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echo ""
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echo -e "${BLUE}Test Print:${NC}"
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echo " • Print at 25% scale (A0→A4, 36×48→Letter)"
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echo " • Check readability from 2-3 feet"
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|
+
echo " • Verify colors printed accurately"
|
|
189
|
+
echo ""
|
|
190
|
+
|
|
191
|
+
echo -e "${BLUE}Digital Checks:${NC}"
|
|
192
|
+
echo " • View at 100% zoom in PDF viewer"
|
|
193
|
+
echo " • Test on different screens/devices"
|
|
194
|
+
echo " • Verify QR codes work with scanner app"
|
|
195
|
+
echo ""
|
|
196
|
+
|
|
197
|
+
echo -e "${BLUE}Proofreading:${NC}"
|
|
198
|
+
echo " • Spell-check all text"
|
|
199
|
+
echo " • Verify author names and affiliations"
|
|
200
|
+
echo " • Confirm all statistics and numbers"
|
|
201
|
+
echo " • Ask colleague to review"
|
|
202
|
+
echo ""
|
|
203
|
+
|
|
204
|
+
# 8. Summary
|
|
205
|
+
echo -e "${BLUE}═══════════════════════════════════════════════${NC}"
|
|
206
|
+
echo -e "${BLUE} Quality Check Complete${NC}"
|
|
207
|
+
echo -e "${BLUE}═══════════════════════════════════════════════${NC}"
|
|
208
|
+
echo ""
|
|
209
|
+
echo -e "Review the checks above and complete manual verification."
|
|
210
|
+
echo -e "For full checklist, see: ${BLUE}assets/poster_quality_checklist.md${NC}"
|
|
211
|
+
echo ""
|
|
212
|
+
|
|
213
|
+
exit 0
|
|
214
|
+
|