medsci-skills 4.1.0
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.
- package/LICENSE +50 -0
- package/README.md +602 -0
- package/README_FIRST.md +27 -0
- package/bin/medsci-skills.js +159 -0
- package/installers/install-macos.command +19 -0
- package/installers/install-windows.cmd +26 -0
- package/installers/install-windows.ps1 +17 -0
- package/installers/install.py +218 -0
- package/metadata/skills_catalog.json +452 -0
- package/package.json +48 -0
- package/skills/academic-aio/SKILL.md +408 -0
- package/skills/academic-aio/references/case_studies/kjr_mllm_2025.md +82 -0
- package/skills/academic-aio/references/checklists/AIO_GENERAL.md +354 -0
- package/skills/academic-aio/references/journal_summarybox_templates.yaml +126 -0
- package/skills/academic-aio/references/oac_funding_checklist.yaml +129 -0
- package/skills/academic-aio/references/reporting_guideline_mapping.md +39 -0
- package/skills/academic-aio/references/schema_markup_templates/CodeRepository.jsonld +32 -0
- package/skills/academic-aio/references/schema_markup_templates/Dataset.jsonld +36 -0
- package/skills/academic-aio/references/schema_markup_templates/Person.jsonld +30 -0
- package/skills/academic-aio/references/schema_markup_templates/README.md +43 -0
- package/skills/academic-aio/references/schema_markup_templates/ScholarlyArticle.jsonld +55 -0
- package/skills/academic-aio/scripts/batch_metadata_audit.py +169 -0
- package/skills/academic-aio/scripts/validate_schema.py +118 -0
- package/skills/academic-aio/skill.yml +36 -0
- package/skills/academic-aio/templates/aio_audit_checklist.md.j2 +108 -0
- package/skills/add-journal/SKILL.md +482 -0
- package/skills/add-journal/skill.yml +33 -0
- package/skills/analyze-stats/SKILL.md +598 -0
- package/skills/analyze-stats/references/analysis_guides/missing_data.md +109 -0
- package/skills/analyze-stats/references/analysis_guides/nhis_icd10_mapping.md +247 -0
- package/skills/analyze-stats/references/analysis_guides/propensity_score.md +132 -0
- package/skills/analyze-stats/references/analysis_guides/regression.md +115 -0
- package/skills/analyze-stats/references/analysis_guides/repeated_measures.md +160 -0
- package/skills/analyze-stats/references/analysis_guides/survey_weighted.md +366 -0
- package/skills/analyze-stats/references/analysis_guides/test_selection.md +86 -0
- package/skills/analyze-stats/references/style/figure_style.mplstyle +69 -0
- package/skills/analyze-stats/references/style/theme_publication.R +147 -0
- package/skills/analyze-stats/references/table-standards/journal-profiles/ajr.yaml +51 -0
- package/skills/analyze-stats/references/table-standards/journal-profiles/european_radiology.yaml +55 -0
- package/skills/analyze-stats/references/table-standards/journal-profiles/jama.yaml +66 -0
- package/skills/analyze-stats/references/table-standards/journal-profiles/lancet.yaml +57 -0
- package/skills/analyze-stats/references/table-standards/journal-profiles/nejm.yaml +51 -0
- package/skills/analyze-stats/references/table-standards/journal-profiles/radiology.yaml +66 -0
- package/skills/analyze-stats/references/table-standards/table-standards.md +287 -0
- package/skills/analyze-stats/references/table-standards/table-types/diagnostic_accuracy.md +36 -0
- package/skills/analyze-stats/references/table-standards/table-types/meta_analysis.md +58 -0
- package/skills/analyze-stats/references/table-standards/table-types/model_comparison.md +36 -0
- package/skills/analyze-stats/references/table-standards/table-types/regression_results.md +50 -0
- package/skills/analyze-stats/references/table-standards/table-types/table1_demographics.md +51 -0
- package/skills/analyze-stats/references/table-standards/tool-comparison.md +79 -0
- package/skills/analyze-stats/references/templates/agreement_analysis.py +436 -0
- package/skills/analyze-stats/references/templates/dca_plot.R +237 -0
- package/skills/analyze-stats/references/templates/diagnostic_accuracy.py +401 -0
- package/skills/analyze-stats/references/templates/dta_meta_analysis.R +384 -0
- package/skills/analyze-stats/references/templates/forest_plot.py +412 -0
- package/skills/analyze-stats/references/templates/likert_summary.py +356 -0
- package/skills/analyze-stats/references/templates/meta_analysis.R +365 -0
- package/skills/analyze-stats/references/templates/propensity_score.py +478 -0
- package/skills/analyze-stats/references/templates/regression.py +425 -0
- package/skills/analyze-stats/references/templates/repeated_measures.py +434 -0
- package/skills/analyze-stats/references/templates/sample_size.R +382 -0
- package/skills/analyze-stats/references/templates/survey_weighted_analysis.py +411 -0
- package/skills/analyze-stats/references/templates/survival_analysis.py +325 -0
- package/skills/analyze-stats/references/templates/table1_demographics.py +287 -0
- package/skills/analyze-stats/scripts/check_generated_code.py +335 -0
- package/skills/analyze-stats/skill.yml +38 -0
- package/skills/analyze-stats/tests/fixtures/gen_bad.R +16 -0
- package/skills/analyze-stats/tests/fixtures/gen_bad.py +24 -0
- package/skills/analyze-stats/tests/fixtures/gen_clean.py +21 -0
- package/skills/analyze-stats/tests/test_generated_code.sh +59 -0
- package/skills/analyze-stats/tests/test_survival_template.sh +53 -0
- package/skills/author-strategy/SKILL.md +117 -0
- package/skills/author-strategy/analyze_patterns.py +303 -0
- package/skills/author-strategy/fetch_pubmed.py +374 -0
- package/skills/author-strategy/skill.yml +34 -0
- package/skills/batch-cohort/SKILL.md +223 -0
- package/skills/batch-cohort/references/base_template_knhanes.R +210 -0
- package/skills/batch-cohort/references/batch_template_generator.R +222 -0
- package/skills/batch-cohort/references/variable_coding_registry.md +136 -0
- package/skills/batch-cohort/skill.yml +35 -0
- package/skills/calc-sample-size/SKILL.md +491 -0
- package/skills/calc-sample-size/references/formulas.md +655 -0
- package/skills/calc-sample-size/references/observational_cohort.md +49 -0
- package/skills/calc-sample-size/skill.yml +51 -0
- package/skills/check-reporting/SKILL.md +534 -0
- package/skills/check-reporting/references/LICENSES.md +41 -0
- package/skills/check-reporting/references/checklists/AMSTAR2.md +54 -0
- package/skills/check-reporting/references/checklists/ARRIVE_2.md +234 -0
- package/skills/check-reporting/references/checklists/CARE.md +102 -0
- package/skills/check-reporting/references/checklists/CLAIM_2024.md +128 -0
- package/skills/check-reporting/references/checklists/CLEAR.md +113 -0
- package/skills/check-reporting/references/checklists/CONSORT.md +86 -0
- package/skills/check-reporting/references/checklists/COSMIN_RoB.md +136 -0
- package/skills/check-reporting/references/checklists/GRRAS.md +61 -0
- package/skills/check-reporting/references/checklists/MI_CLEAR_LLM.md +167 -0
- package/skills/check-reporting/references/checklists/MOOSE.md +85 -0
- package/skills/check-reporting/references/checklists/NOS.md +88 -0
- package/skills/check-reporting/references/checklists/PRISMA_2020.md +135 -0
- package/skills/check-reporting/references/checklists/PRISMA_DTA.md +36 -0
- package/skills/check-reporting/references/checklists/PRISMA_P.md +56 -0
- package/skills/check-reporting/references/checklists/PROBAST.md +75 -0
- package/skills/check-reporting/references/checklists/PROBAST_AI.md +130 -0
- package/skills/check-reporting/references/checklists/QUADAS2.md +77 -0
- package/skills/check-reporting/references/checklists/QUADAS_C.md +131 -0
- package/skills/check-reporting/references/checklists/ROBINS_E.md +179 -0
- package/skills/check-reporting/references/checklists/ROBINS_I.md +87 -0
- package/skills/check-reporting/references/checklists/ROBIS.md +114 -0
- package/skills/check-reporting/references/checklists/ROB_ME.md +126 -0
- package/skills/check-reporting/references/checklists/RoB2.md +79 -0
- package/skills/check-reporting/references/checklists/RoB_NMA.md +96 -0
- package/skills/check-reporting/references/checklists/SPIRIT.md +112 -0
- package/skills/check-reporting/references/checklists/SQUIRE_2.md +68 -0
- package/skills/check-reporting/references/checklists/STARD.md +129 -0
- package/skills/check-reporting/references/checklists/STARD_AI.md +211 -0
- package/skills/check-reporting/references/checklists/STROBE.md +80 -0
- package/skills/check-reporting/references/checklists/SWiM.md +33 -0
- package/skills/check-reporting/references/checklists/TRIPOD.md +157 -0
- package/skills/check-reporting/references/checklists/TRIPOD_AI.md +140 -0
- package/skills/check-reporting/references/step4c_registration_timing.md +93 -0
- package/skills/check-reporting/references/step4d_prisma_figure_audit.md +137 -0
- package/skills/check-reporting/scripts/check_checklist_exists.py +183 -0
- package/skills/check-reporting/scripts/check_checklist_version.py +168 -0
- package/skills/check-reporting/scripts/check_framework_naming.py +206 -0
- package/skills/check-reporting/scripts/check_prisma_figure.py +209 -0
- package/skills/check-reporting/scripts/prisma_cascade_check.py +274 -0
- package/skills/check-reporting/skill.yml +41 -0
- package/skills/check-reporting/tests/fixtures/framework_bad.md +8 -0
- package/skills/check-reporting/tests/fixtures/framework_clean.md +7 -0
- package/skills/check-reporting/tests/test_checklist_fail_fast.sh +77 -0
- package/skills/check-reporting/tests/test_checklist_version.sh +72 -0
- package/skills/check-reporting/tests/test_framework_naming.sh +45 -0
- package/skills/check-reporting/tests/test_prisma_cascade.sh +104 -0
- package/skills/clean-data/SKILL.md +180 -0
- package/skills/clean-data/references/cleaning_patterns.md +299 -0
- package/skills/clean-data/references/profiling_template.py +304 -0
- package/skills/clean-data/scripts/check_structural_zero.py +174 -0
- package/skills/clean-data/skill.yml +35 -0
- package/skills/clean-data/tests/fixtures/smoking.csv +8 -0
- package/skills/clean-data/tests/test_structural_zero.sh +49 -0
- package/skills/cross-national/SKILL.md +264 -0
- package/skills/cross-national/skill.yml +37 -0
- package/skills/define-variables/SKILL.md +146 -0
- package/skills/define-variables/references/common_definitions.md +190 -0
- package/skills/define-variables/skill.yml +34 -0
- package/skills/define-variables/templates/variable_operationalization.md +64 -0
- package/skills/deidentify/SKILL.md +203 -0
- package/skills/deidentify/deidentify.py +1224 -0
- package/skills/deidentify/locales/_template.json +45 -0
- package/skills/deidentify/locales/au.json +43 -0
- package/skills/deidentify/locales/ca.json +44 -0
- package/skills/deidentify/locales/cn.json +47 -0
- package/skills/deidentify/locales/de.json +48 -0
- package/skills/deidentify/locales/fr.json +48 -0
- package/skills/deidentify/locales/in.json +48 -0
- package/skills/deidentify/locales/jp.json +48 -0
- package/skills/deidentify/locales/kr.json +48 -0
- package/skills/deidentify/locales/uk.json +45 -0
- package/skills/deidentify/locales/us.json +43 -0
- package/skills/deidentify/references/date_shift_guide.md +82 -0
- package/skills/deidentify/references/hipaa_18_identifiers.md +48 -0
- package/skills/deidentify/references/korean_phi_patterns.md +135 -0
- package/skills/deidentify/skill.yml +43 -0
- package/skills/deidentify/tests/README.md +26 -0
- package/skills/deidentify/tests/test_clean.csv +16 -0
- package/skills/deidentify/tests/test_edge_cases.csv +11 -0
- package/skills/deidentify/tests/test_phi_korean.csv +11 -0
- package/skills/design-ai-benchmarking/SKILL.md +214 -0
- package/skills/design-ai-benchmarking/references/benchmark_export_schema.json +69 -0
- package/skills/design-ai-benchmarking/references/elicitation_rubric_template.md +37 -0
- package/skills/design-ai-benchmarking/skill.yml +38 -0
- package/skills/design-study/SKILL.md +298 -0
- package/skills/design-study/skill.yml +33 -0
- package/skills/fill-icmje-coi/SKILL.md +216 -0
- package/skills/fill-icmje-coi/scripts/fill_icmje_coi.py +140 -0
- package/skills/fill-icmje-coi/skill.yml +35 -0
- package/skills/fill-icmje-coi/templates/icmje_coi_seed_synthetic.docx +0 -0
- package/skills/fill-protocol/SKILL.md +248 -0
- package/skills/fill-protocol/examples/example_irb_template.yaml +53 -0
- package/skills/fill-protocol/references/best_practices.md +121 -0
- package/skills/fill-protocol/scripts/doc_to_docx.py +111 -0
- package/skills/fill-protocol/scripts/fill_form.py +611 -0
- package/skills/fill-protocol/scripts/inspect_template.py +61 -0
- package/skills/fill-protocol/setup.sh +162 -0
- package/skills/fill-protocol/skill.yml +37 -0
- package/skills/find-cohort-gap/SKILL.md +309 -0
- package/skills/find-cohort-gap/references/cohort_profile_template.md +93 -0
- package/skills/find-cohort-gap/references/onepager_template.md +84 -0
- package/skills/find-cohort-gap/references/pattern_scoring_rubric.md +169 -0
- package/skills/find-cohort-gap/references/saturation_query_templates.md +143 -0
- package/skills/find-cohort-gap/skill.yml +35 -0
- package/skills/find-journal/POLICY.md +87 -0
- package/skills/find-journal/SKILL.md +340 -0
- package/skills/find-journal/references/journal_profiles/AJNR.md +29 -0
- package/skills/find-journal/references/journal_profiles/AJR.md +30 -0
- package/skills/find-journal/references/journal_profiles/Abdominal_Radiology.md +30 -0
- package/skills/find-journal/references/journal_profiles/Academic_Radiology.md +30 -0
- package/skills/find-journal/references/journal_profiles/Annals_of_Internal_Medicine.md +33 -0
- package/skills/find-journal/references/journal_profiles/Artificial_Intelligence_in_Medicine.md +28 -0
- package/skills/find-journal/references/journal_profiles/BMC_Medicine.md +31 -0
- package/skills/find-journal/references/journal_profiles/British_Journal_of_Radiology.md +39 -0
- package/skills/find-journal/references/journal_profiles/CVIR.md +30 -0
- package/skills/find-journal/references/journal_profiles/Chest.md +39 -0
- package/skills/find-journal/references/journal_profiles/Clinical_Radiology.md +30 -0
- package/skills/find-journal/references/journal_profiles/Clinical_and_Molecular_Hepatology.md +32 -0
- package/skills/find-journal/references/journal_profiles/Diabetes_Metabolism_Journal.md +36 -0
- package/skills/find-journal/references/journal_profiles/Diagnostic_and_Interventional_Radiology.md +32 -0
- package/skills/find-journal/references/journal_profiles/Endocrinology_and_Metabolism.md +37 -0
- package/skills/find-journal/references/journal_profiles/European_Journal_of_Preventive_Cardiology.md +39 -0
- package/skills/find-journal/references/journal_profiles/European_Radiology.md +29 -0
- package/skills/find-journal/references/journal_profiles/Hepatology_Communications.md +40 -0
- package/skills/find-journal/references/journal_profiles/Hepatology_International.md +37 -0
- package/skills/find-journal/references/journal_profiles/IEEE_JBHI.md +28 -0
- package/skills/find-journal/references/journal_profiles/IEEE_TMI.md +28 -0
- package/skills/find-journal/references/journal_profiles/INSI.md +29 -0
- package/skills/find-journal/references/journal_profiles/Investigative_Radiology.md +25 -0
- package/skills/find-journal/references/journal_profiles/JACC_Advances.md +41 -0
- package/skills/find-journal/references/journal_profiles/JACC_Asia.md +30 -0
- package/skills/find-journal/references/journal_profiles/JACR.md +28 -0
- package/skills/find-journal/references/journal_profiles/JAMA.md +40 -0
- package/skills/find-journal/references/journal_profiles/JAMA_Network_Open.md +30 -0
- package/skills/find-journal/references/journal_profiles/JCSM.md +39 -0
- package/skills/find-journal/references/journal_profiles/JKMS.md +32 -0
- package/skills/find-journal/references/journal_profiles/JMIR.md +29 -0
- package/skills/find-journal/references/journal_profiles/JMIR_Medical_Education.md +29 -0
- package/skills/find-journal/references/journal_profiles/JNIS.md +35 -0
- package/skills/find-journal/references/journal_profiles/JVIR.md +31 -0
- package/skills/find-journal/references/journal_profiles/Journal_of_Biomedical_Informatics.md +29 -0
- package/skills/find-journal/references/journal_profiles/Journal_of_Clinical_Endocrinology_and_Metabolism.md +40 -0
- package/skills/find-journal/references/journal_profiles/Journal_of_Magnetic_Resonance_Imaging.md +30 -0
- package/skills/find-journal/references/journal_profiles/Journal_of_Nuclear_Medicine.md +31 -0
- package/skills/find-journal/references/journal_profiles/Journal_of_Stroke.md +32 -0
- package/skills/find-journal/references/journal_profiles/KJR.md +38 -0
- package/skills/find-journal/references/journal_profiles/Korean_Circulation_Journal.md +38 -0
- package/skills/find-journal/references/journal_profiles/Korean_Journal_of_Internal_Medicine.md +36 -0
- package/skills/find-journal/references/journal_profiles/Lancet_Diabetes_and_Endocrinology.md +40 -0
- package/skills/find-journal/references/journal_profiles/Lancet_Gastroenterology_and_Hepatology.md +49 -0
- package/skills/find-journal/references/journal_profiles/Lancet_Infectious_Diseases.md +38 -0
- package/skills/find-journal/references/journal_profiles/Lancet_Neurology.md +39 -0
- package/skills/find-journal/references/journal_profiles/Lancet_Oncology.md +40 -0
- package/skills/find-journal/references/journal_profiles/Lancet_Psychiatry.md +38 -0
- package/skills/find-journal/references/journal_profiles/Lancet_Public_Health.md +30 -0
- package/skills/find-journal/references/journal_profiles/Lancet_Respiratory_Medicine.md +39 -0
- package/skills/find-journal/references/journal_profiles/Liver_International.md +33 -0
- package/skills/find-journal/references/journal_profiles/Medical_Image_Analysis.md +28 -0
- package/skills/find-journal/references/journal_profiles/NEJM.md +33 -0
- package/skills/find-journal/references/journal_profiles/Nature_Machine_Intelligence.md +31 -0
- package/skills/find-journal/references/journal_profiles/Nature_Medicine.md +39 -0
- package/skills/find-journal/references/journal_profiles/Neuroradiology.md +31 -0
- package/skills/find-journal/references/journal_profiles/Nutrition_Metabolism_and_Cardiovascular_Diseases.md +39 -0
- package/skills/find-journal/references/journal_profiles/PLOS_Medicine.md +32 -0
- package/skills/find-journal/references/journal_profiles/RYAI.md +28 -0
- package/skills/find-journal/references/journal_profiles/Radiology.md +29 -0
- package/skills/find-journal/references/journal_profiles/Skeletal_Radiology.md +31 -0
- package/skills/find-journal/references/journal_profiles/Stroke.md +37 -0
- package/skills/find-journal/references/journal_profiles/The_BMJ.md +31 -0
- package/skills/find-journal/references/journal_profiles/The_Lancet.md +31 -0
- package/skills/find-journal/references/journal_profiles/The_Lancet_Digital_Health.md +29 -0
- package/skills/find-journal/references/journal_profiles/World_Journal_of_Hepatology.md +53 -0
- package/skills/find-journal/references/journal_profiles/npj_Digital_Medicine.md +29 -0
- package/skills/find-journal/skill.yml +34 -0
- package/skills/fulltext-retrieval/SKILL.md +174 -0
- package/skills/fulltext-retrieval/fetch_oa.py +433 -0
- package/skills/fulltext-retrieval/pdf_to_md.py +160 -0
- package/skills/fulltext-retrieval/skill.yml +41 -0
- package/skills/generate-codebook/SKILL.md +155 -0
- package/skills/generate-codebook/references/codebook_schema.md +76 -0
- package/skills/generate-codebook/scripts/generate_codebook.py +278 -0
- package/skills/generate-codebook/skill.yml +35 -0
- package/skills/generate-codebook/tests/test_generate_codebook.sh +76 -0
- package/skills/grant-builder/SKILL.md +251 -0
- package/skills/grant-builder/skill.yml +34 -0
- package/skills/humanize/SKILL.md +251 -0
- package/skills/humanize/references/ai_patterns.md +571 -0
- package/skills/humanize/skill.yml +33 -0
- package/skills/intake-project/SKILL.md +264 -0
- package/skills/intake-project/skill.yml +34 -0
- package/skills/lit-sync/SKILL.md +448 -0
- package/skills/lit-sync/references/locale/ko/note_templates.md +110 -0
- package/skills/lit-sync/skill.yml +52 -0
- package/skills/lit-sync/tests/test_poll_logic.sh +92 -0
- package/skills/ma-scout/SKILL.md +640 -0
- package/skills/ma-scout/references/project_readme_template.md +95 -0
- package/skills/ma-scout/references/project_readme_template_ko.md +82 -0
- package/skills/ma-scout/skill.yml +33 -0
- package/skills/make-figures/SKILL.md +957 -0
- package/skills/make-figures/references/critic_rubrics/data_plot.md +166 -0
- package/skills/make-figures/references/critic_rubrics/flow_diagram.md +169 -0
- package/skills/make-figures/references/design_principles.md +181 -0
- package/skills/make-figures/references/exemplar_diagrams/README.md +65 -0
- package/skills/make-figures/references/exemplar_diagrams/consort/README.md +15 -0
- package/skills/make-figures/references/exemplar_diagrams/consort/template_input.yaml +37 -0
- package/skills/make-figures/references/exemplar_diagrams/consort/template_output.pdf +0 -0
- package/skills/make-figures/references/exemplar_diagrams/consort/template_output.png +0 -0
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- package/skills/self-review/tests/test_confounding_completeness.sh +66 -0
- package/skills/self-review/tests/test_panel_diversity.sh +55 -0
- package/skills/self-review/tests/test_panel_mode.sh +69 -0
- package/skills/self-review/tests/test_reference_adequacy.sh +68 -0
- package/skills/self-review/tests/test_reviewer_team_consistency.sh +138 -0
- package/skills/self-review/tests/test_scope_coherence.sh +46 -0
- package/skills/setup-medsci/SKILL.md +110 -0
- package/skills/setup-medsci/references/setup-checklist.md +51 -0
- package/skills/setup-medsci/skill.yml +30 -0
- package/skills/sync-submission/SKILL.md +382 -0
- package/skills/sync-submission/scripts/author_registry_example.yaml +36 -0
- package/skills/sync-submission/scripts/blind_sweep.py +203 -0
- package/skills/sync-submission/scripts/check_asset_anonymization.py +300 -0
- package/skills/sync-submission/scripts/check_cross_artifact_stale.py +211 -0
- package/skills/sync-submission/scripts/cover_letter_drift_check.py +451 -0
- package/skills/sync-submission/scripts/cross_document_n_check.py +486 -0
- package/skills/sync-submission/scripts/detect_copy_divergence.py +136 -0
- package/skills/sync-submission/scripts/preflight_gate.py +458 -0
- package/skills/sync-submission/scripts/scope_drift_check.py +362 -0
- package/skills/sync-submission/scripts/sync_submission.py +169 -0
- package/skills/sync-submission/skill.yml +43 -0
- package/skills/sync-submission/tests/fixtures/copy_ok.md +5 -0
- package/skills/sync-submission/tests/fixtures/copy_stale.md +5 -0
- package/skills/sync-submission/tests/fixtures/ssot.md +5 -0
- package/skills/sync-submission/tests/test_asset_anonymization.sh +99 -0
- package/skills/sync-submission/tests/test_copy_divergence.sh +44 -0
- package/skills/sync-submission/tests/test_cross_artifact_stale.sh +80 -0
- package/skills/sync-submission/tests/test_cross_document_n.sh +132 -0
- package/skills/sync-submission/tests/test_preflight_gate.sh +112 -0
- package/skills/sync-submission/tests/test_scope_drift.sh +122 -0
- package/skills/sync-submission/tests/test_vN_docx_assertion.sh +51 -0
- package/skills/verify-refs/SKILL.md +177 -0
- package/skills/verify-refs/references/manual_checkpoint_guide.md +100 -0
- package/skills/verify-refs/scripts/verify_cli.sh +62 -0
- package/skills/verify-refs/scripts/verify_refs.py +782 -0
- package/skills/verify-refs/skill.yml +44 -0
- package/skills/verify-refs/tests/fixtures/pagination_placeholder.bib +17 -0
- package/skills/verify-refs/tests/test_pagination_placeholder.sh +42 -0
- package/skills/version-dataset/SKILL.md +143 -0
- package/skills/version-dataset/references/manifest_schema.md +72 -0
- package/skills/version-dataset/scripts/version_dataset.py +242 -0
- package/skills/version-dataset/skill.yml +35 -0
- package/skills/version-dataset/tests/test_version_dataset.sh +52 -0
- package/skills/write-paper/SKILL.md +1148 -0
- package/skills/write-paper/references/exemplar_methods/README.md +38 -0
- package/skills/write-paper/references/exemplar_methods/ai_validation_tripod_claim.md +47 -0
- package/skills/write-paper/references/exemplar_methods/diagnostic_accuracy_stard.md +50 -0
- package/skills/write-paper/references/exemplar_methods/observational_cohort_strobe.md +43 -0
- package/skills/write-paper/references/journal_profiles/AJNR.md +185 -0
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- package/skills/write-paper/references/journal_profiles/Abdominal_Radiology.md +139 -0
- package/skills/write-paper/references/journal_profiles/Academic_Radiology.md +90 -0
- package/skills/write-paper/references/journal_profiles/Annals_of_Internal_Medicine.md +150 -0
- package/skills/write-paper/references/journal_profiles/Artificial_Intelligence_in_Medicine.md +82 -0
- package/skills/write-paper/references/journal_profiles/British_Journal_of_Radiology.md +161 -0
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- package/skills/write-paper/references/journal_profiles/Chest.md +270 -0
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- package/skills/write-paper/references/journal_profiles/Clinical_and_Molecular_Hepatology.md +147 -0
- package/skills/write-paper/references/journal_profiles/Diabetes_Metabolism_Journal.md +163 -0
- package/skills/write-paper/references/journal_profiles/Diagnostic_and_Interventional_Radiology.md +216 -0
- package/skills/write-paper/references/journal_profiles/Endocrinology_and_Metabolism.md +167 -0
- package/skills/write-paper/references/journal_profiles/European_Journal_of_Preventive_Cardiology.md +192 -0
- package/skills/write-paper/references/journal_profiles/European_Radiology.md +159 -0
- package/skills/write-paper/references/journal_profiles/Hepatology_Communications.md +110 -0
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- package/skills/write-paper/references/journal_profiles/World_Journal_of_Hepatology.md +106 -0
- package/skills/write-paper/references/journal_profiles/npj_Digital_Medicine.md +93 -0
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#!/usr/bin/env python3
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"""Nature/Lancet style PPTX builder — academic lecture / journal club / conference.
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Generic template — pass slide content via builder functions. Speaker notes are
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written in the user's preferred language (English by default; a Korean narrative
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register is also supported for Korean presenters); slide body in English.
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Color palette + typography + layout grid per:
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references/slide_visual_styles/nature_lancet.md
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Mac PowerPoint compatibility per:
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~/.claude/rules/pptx-mac-compatibility.md
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→ run fix_app_xml() after final save (function included below)
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Usage (illustrative):
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from build_pptx_nature_lancet import (
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new_presentation, add_title_slide, add_toc_slide, add_section_divider,
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add_transition_slide, add_content_slide, add_closing_slide,
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fix_app_xml,
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)
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prs = new_presentation()
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add_title_slide(prs,
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eyebrow="REVIEW LECTURE",
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title="<Lecture title in English>",
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subtitle="<One-line scope or lighthouse-paper subtitle>",
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meta_top="<Course> · <Instructor> · <Date>",
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meta_bottom="Presenter <Name> · <Department / Affiliation>",
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notes="<speaker notes in the user's preferred language>")
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add_toc_slide(prs, sections=[
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("01", "<Section A title>", "<one-line summary>", "5 min"),
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("02", "<Section B title>", "<one-line summary>", "8 min"),
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# ...
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], notes="<...>", page_brand="<YEAR · COURSE NAME>")
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add_section_divider(prs, num="01", title="<Section A title>",
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subtitle="<lighthouse paper or section theme>", time_min=5)
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add_content_slide(prs,
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eyebrow="<COURSE / TOPIC LABEL>",
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title="<Sentence-headline title>",
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subtitle="<Author et al, Journal YYYY — n=...>",
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bullets=[
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"**Bold** main bullet",
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" Sub bullet (prefix with 2 spaces)",
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"Another main bullet with *italic*",
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],
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figure_path="figures/<your_fig>.png",
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fig_caption="<Short caption>",
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footnote="<Author et al, Journal YYYY>",
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page_brand="<YEAR · COURSE NAME>",
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notes="<notes in the user's preferred language>")
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add_closing_slide(prs, title="Take-home messages", bullets=[...], notes="...")
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out = Path("output.pptx")
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prs.save(out)
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fix_app_xml(out)
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"""
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from __future__ import annotations
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import re
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import shutil
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import zipfile
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from pathlib import Path
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from typing import Iterable, Sequence
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from pptx import Presentation
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from pptx.util import Inches, Pt, Emu
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from pptx.enum.text import PP_ALIGN, MSO_ANCHOR
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from pptx.dml.color import RGBColor
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from pptx.enum.shapes import MSO_SHAPE
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# ============================================================================
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# Style tokens — keep in sync with references/slide_visual_styles/nature_lancet.md
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# ============================================================================
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COLOR_NAVY = RGBColor(0x1B, 0x2A, 0x4E)
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COLOR_NAVY_LIGHT = RGBColor(0x3F, 0x5A, 0x8C)
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COLOR_TEXT = RGBColor(0x21, 0x25, 0x2B)
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COLOR_TEXT_SUB = RGBColor(0x4A, 0x52, 0x5C)
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COLOR_MUTED = RGBColor(0x8A, 0x92, 0x9E)
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COLOR_HAIRLINE = RGBColor(0xCC, 0xD0, 0xD6)
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COLOR_HIGHLIGHT = RGBColor(0xB8, 0x3E, 0x3A)
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COLOR_WHITE = RGBColor(0xFF, 0xFF, 0xFF)
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COLOR_BG_SOFT = RGBColor(0xF8, 0xF9, 0xFB)
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COLOR_DIVIDER_BG = RGBColor(0x12, 0x1D, 0x36)
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COLOR_DIVIDER_SUB = RGBColor(0xC0, 0xCB, 0xDC)
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SLIDE_W = Inches(13.333)
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FONT_KR = "Pretendard"
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FONT_EN = "Inter"
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# ============================================================================
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# ============================================================================
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def set_run(run, *, size: float = 20, bold: bool = False, italic: bool = False,
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color: RGBColor = COLOR_TEXT, ko: str = FONT_KR, en: str = FONT_EN,
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"""Apply Nature/Lancet font + size + color, with eastAsia attribute for Korean."""
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run.font.size = Pt(size)
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run.font.bold = bold
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run.font.italic = italic
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run.font.color.rgb = color
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run.font.name = en
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rPr = run._r.get_or_add_rPr()
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for ea in rPr.findall(f"{{{A_NS}}}ea"):
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rPr.remove(ea)
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ea = etree.SubElement(rPr, f"{{{A_NS}}}ea")
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ea.set("typeface", ko)
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if letter_space is not None:
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rPr.set("spc", str(letter_space))
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_MD_PATTERN = re.compile(r"(\*\*[^*\n]+\*\*|\*[^*\n]+\*)")
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def add_styled(p, text: str, *, size: float = 20, color: RGBColor = COLOR_TEXT,
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ko: str = FONT_KR, en: str = FONT_EN) -> None:
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"""Add a paragraph run with minimal markdown (**bold** / *italic*) parsed inline."""
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for part in _MD_PATTERN.split(text):
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continue
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r = p.add_run()
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if part.startswith("**") and part.endswith("**"):
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r.text = part[2:-2]
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set_run(r, size=size, bold=True, color=color, ko=ko, en=en)
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elif part.startswith("*") and part.endswith("*") and len(part) > 2:
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r.text = part[1:-1]
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set_run(r, size=size, italic=True, color=color, ko=ko, en=en)
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else:
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r.text = part
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set_run(r, size=size, color=color, ko=ko, en=en)
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def add_notes(slide, text: str | None) -> None:
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"""Inject speaker notes in the user's preferred language (with **bold**/*italic* parsed per run)."""
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if not text:
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return
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tf = slide.notes_slide.notes_text_frame
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tf.text = ""
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for i, line in enumerate(text.strip().split("\n")):
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if not line.strip():
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r = p.add_run(); r.text = " "
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set_run(r, size=12)
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add_styled(p, line, size=13)
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# ============================================================================
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# Presentation initialization
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# ============================================================================
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def new_presentation(width_in: float = 13.333, height_in: float = 7.5) -> Presentation:
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"""Create a 16:9 widescreen Presentation with the Nature/Lancet defaults."""
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prs = Presentation()
|
|
167
|
+
prs.slide_width = Inches(width_in)
|
|
168
|
+
prs.slide_height = Inches(height_in)
|
|
169
|
+
return prs
|
|
170
|
+
|
|
171
|
+
|
|
172
|
+
def _blank(prs: Presentation):
|
|
173
|
+
"""Return a blank-layout slide (layouts[6] is blank in default template)."""
|
|
174
|
+
return prs.slides.add_slide(prs.slide_layouts[6])
|
|
175
|
+
|
|
176
|
+
|
|
177
|
+
# ============================================================================
|
|
178
|
+
# Slide builders
|
|
179
|
+
# ============================================================================
|
|
180
|
+
|
|
181
|
+
def add_title_slide(prs: Presentation, *,
|
|
182
|
+
eyebrow: str,
|
|
183
|
+
title: str,
|
|
184
|
+
subtitle: str | None = None,
|
|
185
|
+
meta_top: str | None = None,
|
|
186
|
+
meta_bottom: str | None = None,
|
|
187
|
+
notes: str | None = None):
|
|
188
|
+
s = _blank(prs)
|
|
189
|
+
|
|
190
|
+
bar = s.shapes.add_shape(MSO_SHAPE.RECTANGLE,
|
|
191
|
+
Inches(0.7), Inches(2.2), Emu(40000), Inches(3.5))
|
|
192
|
+
bar.fill.solid(); bar.fill.fore_color.rgb = COLOR_NAVY
|
|
193
|
+
bar.line.fill.background()
|
|
194
|
+
|
|
195
|
+
eye = s.shapes.add_textbox(Inches(1.1), Inches(2.2), Inches(10), Inches(0.5))
|
|
196
|
+
p = eye.text_frame.paragraphs[0]
|
|
197
|
+
r = p.add_run(); r.text = eyebrow
|
|
198
|
+
set_run(r, size=14, bold=True, color=COLOR_HIGHLIGHT, letter_space="300")
|
|
199
|
+
|
|
200
|
+
box = s.shapes.add_textbox(Inches(1.1), Inches(2.7), Inches(11.5), Inches(2.5))
|
|
201
|
+
tf = box.text_frame; tf.word_wrap = True
|
|
202
|
+
p = tf.paragraphs[0]; p.alignment = PP_ALIGN.LEFT
|
|
203
|
+
r = p.add_run(); r.text = title
|
|
204
|
+
set_run(r, size=48, bold=True, color=COLOR_NAVY)
|
|
205
|
+
p.space_after = Pt(8)
|
|
206
|
+
if subtitle:
|
|
207
|
+
p2 = tf.add_paragraph(); p2.alignment = PP_ALIGN.LEFT
|
|
208
|
+
r2 = p2.add_run(); r2.text = subtitle
|
|
209
|
+
set_run(r2, size=18, italic=True, color=COLOR_TEXT_SUB)
|
|
210
|
+
|
|
211
|
+
if meta_top or meta_bottom:
|
|
212
|
+
line = s.shapes.add_shape(MSO_SHAPE.RECTANGLE,
|
|
213
|
+
Inches(1.1), Inches(5.95), Inches(2.0), Emu(8000))
|
|
214
|
+
line.fill.solid(); line.fill.fore_color.rgb = COLOR_NAVY
|
|
215
|
+
line.line.fill.background()
|
|
216
|
+
|
|
217
|
+
sub = s.shapes.add_textbox(Inches(1.1), Inches(6.0), Inches(11.5), Inches(1.0))
|
|
218
|
+
stf = sub.text_frame; stf.word_wrap = True
|
|
219
|
+
rows = [
|
|
220
|
+
(meta_top, 16, True, COLOR_NAVY),
|
|
221
|
+
(meta_bottom, 13, False, COLOR_TEXT_SUB),
|
|
222
|
+
]
|
|
223
|
+
first = True
|
|
224
|
+
for text, sz, bld, col in rows:
|
|
225
|
+
if not text:
|
|
226
|
+
continue
|
|
227
|
+
p = stf.paragraphs[0] if first else stf.add_paragraph()
|
|
228
|
+
first = False
|
|
229
|
+
p.alignment = PP_ALIGN.LEFT
|
|
230
|
+
p.space_after = Pt(4)
|
|
231
|
+
r = p.add_run(); r.text = text
|
|
232
|
+
set_run(r, size=sz, bold=bld, color=col)
|
|
233
|
+
|
|
234
|
+
add_notes(s, notes)
|
|
235
|
+
return s
|
|
236
|
+
|
|
237
|
+
|
|
238
|
+
def add_section_divider(prs: Presentation, *,
|
|
239
|
+
num: str,
|
|
240
|
+
title: str,
|
|
241
|
+
subtitle: str | None = None,
|
|
242
|
+
time_min: int | None = None,
|
|
243
|
+
notes: str | None = None):
|
|
244
|
+
s = _blank(prs)
|
|
245
|
+
|
|
246
|
+
bg = s.shapes.add_shape(MSO_SHAPE.RECTANGLE, Inches(0), Inches(0), SLIDE_W, SLIDE_H)
|
|
247
|
+
bg.fill.solid(); bg.fill.fore_color.rgb = COLOR_DIVIDER_BG
|
|
248
|
+
bg.line.fill.background()
|
|
249
|
+
|
|
250
|
+
accent = s.shapes.add_shape(MSO_SHAPE.RECTANGLE,
|
|
251
|
+
Inches(1.2), Inches(3.0), Emu(15000), Inches(1.8))
|
|
252
|
+
accent.fill.solid(); accent.fill.fore_color.rgb = COLOR_HIGHLIGHT
|
|
253
|
+
accent.line.fill.background()
|
|
254
|
+
|
|
255
|
+
num_box = s.shapes.add_textbox(Inches(1.5), Inches(2.5), Inches(3), Inches(1.5))
|
|
256
|
+
p = num_box.text_frame.paragraphs[0]; p.alignment = PP_ALIGN.LEFT
|
|
257
|
+
r = p.add_run(); r.text = f"SECTION {num}"
|
|
258
|
+
set_run(r, size=18, bold=True, color=COLOR_HIGHLIGHT, letter_space="400")
|
|
259
|
+
|
|
260
|
+
title_box = s.shapes.add_textbox(Inches(1.5), Inches(3.1), Inches(10), Inches(2.5))
|
|
261
|
+
tf = title_box.text_frame; tf.word_wrap = True
|
|
262
|
+
p = tf.paragraphs[0]; p.alignment = PP_ALIGN.LEFT
|
|
263
|
+
r = p.add_run(); r.text = title
|
|
264
|
+
set_run(r, size=52, bold=True, color=COLOR_WHITE)
|
|
265
|
+
p.space_after = Pt(8)
|
|
266
|
+
if subtitle:
|
|
267
|
+
p2 = tf.add_paragraph(); p2.alignment = PP_ALIGN.LEFT
|
|
268
|
+
r2 = p2.add_run(); r2.text = subtitle
|
|
269
|
+
set_run(r2, size=20, italic=True, color=COLOR_DIVIDER_SUB)
|
|
270
|
+
|
|
271
|
+
if time_min is not None:
|
|
272
|
+
time_box = s.shapes.add_textbox(Inches(11.0), Inches(6.5), Inches(2.0), Inches(0.5))
|
|
273
|
+
p = time_box.text_frame.paragraphs[0]; p.alignment = PP_ALIGN.RIGHT
|
|
274
|
+
r = p.add_run(); r.text = f"{time_min} MIN"
|
|
275
|
+
set_run(r, size=13, bold=True, color=COLOR_MUTED, letter_space="500")
|
|
276
|
+
|
|
277
|
+
add_notes(s, notes)
|
|
278
|
+
return s
|
|
279
|
+
|
|
280
|
+
|
|
281
|
+
def add_transition_slide(prs: Presentation, *,
|
|
282
|
+
question: str,
|
|
283
|
+
notes: str | None = None):
|
|
284
|
+
s = _blank(prs)
|
|
285
|
+
bg = s.shapes.add_shape(MSO_SHAPE.RECTANGLE, Inches(0), Inches(0), SLIDE_W, SLIDE_H)
|
|
286
|
+
bg.fill.solid(); bg.fill.fore_color.rgb = COLOR_DIVIDER_BG
|
|
287
|
+
bg.line.fill.background()
|
|
288
|
+
|
|
289
|
+
box = s.shapes.add_textbox(Inches(1.5), Inches(2.5), Inches(10.3), Inches(2.8))
|
|
290
|
+
tf = box.text_frame; tf.word_wrap = True
|
|
291
|
+
tf.vertical_anchor = MSO_ANCHOR.MIDDLE
|
|
292
|
+
p = tf.paragraphs[0]; p.alignment = PP_ALIGN.CENTER
|
|
293
|
+
|
|
294
|
+
q = p.add_run(); q.text = "“ "
|
|
295
|
+
set_run(q, size=72, bold=True, color=COLOR_HIGHLIGHT)
|
|
296
|
+
r = p.add_run(); r.text = question
|
|
297
|
+
set_run(r, size=36, bold=True, color=COLOR_WHITE)
|
|
298
|
+
q2 = p.add_run(); q2.text = " ”"
|
|
299
|
+
set_run(q2, size=72, bold=True, color=COLOR_HIGHLIGHT)
|
|
300
|
+
|
|
301
|
+
add_notes(s, notes)
|
|
302
|
+
return s
|
|
303
|
+
|
|
304
|
+
|
|
305
|
+
def add_content_slide(prs: Presentation, *,
|
|
306
|
+
eyebrow: str,
|
|
307
|
+
title: str,
|
|
308
|
+
subtitle: str | None = None,
|
|
309
|
+
bullets: Sequence[str] = (),
|
|
310
|
+
figure_path: str | Path | None = None,
|
|
311
|
+
fig_caption: str | None = None,
|
|
312
|
+
footnote: str | None = None,
|
|
313
|
+
page_brand: str | None = None,
|
|
314
|
+
notes: str | None = None):
|
|
315
|
+
"""Standard content slide. Bullets prefixed with two spaces become sub-bullets."""
|
|
316
|
+
s = _blank(prs)
|
|
317
|
+
|
|
318
|
+
eye = s.shapes.add_textbox(Inches(0.7), Inches(0.32), Inches(8), Inches(0.4))
|
|
319
|
+
p = eye.text_frame.paragraphs[0]
|
|
320
|
+
r = p.add_run(); r.text = eyebrow
|
|
321
|
+
set_run(r, size=10, bold=True, color=COLOR_MUTED, letter_space="300")
|
|
322
|
+
|
|
323
|
+
title_box = s.shapes.add_textbox(Inches(0.7), Inches(0.75), Inches(12.0), Inches(1.1))
|
|
324
|
+
ttf = title_box.text_frame; ttf.word_wrap = True
|
|
325
|
+
p = ttf.paragraphs[0]; p.alignment = PP_ALIGN.LEFT
|
|
326
|
+
r = p.add_run(); r.text = title
|
|
327
|
+
set_run(r, size=30, bold=True, color=COLOR_NAVY)
|
|
328
|
+
p.space_after = Pt(3)
|
|
329
|
+
if subtitle:
|
|
330
|
+
p2 = ttf.add_paragraph(); p2.alignment = PP_ALIGN.LEFT
|
|
331
|
+
r2 = p2.add_run(); r2.text = subtitle
|
|
332
|
+
set_run(r2, size=15, italic=True, color=COLOR_TEXT_SUB)
|
|
333
|
+
|
|
334
|
+
line = s.shapes.add_shape(MSO_SHAPE.RECTANGLE,
|
|
335
|
+
Inches(0.7), Inches(2.05), Inches(0.6), Emu(20000))
|
|
336
|
+
line.fill.solid(); line.fill.fore_color.rgb = COLOR_HIGHLIGHT
|
|
337
|
+
line.line.fill.background()
|
|
338
|
+
|
|
339
|
+
has_fig = figure_path is not None and Path(figure_path).exists()
|
|
340
|
+
if has_fig:
|
|
341
|
+
bullet_w = Inches(6.8)
|
|
342
|
+
fig_x_in, fig_w_in, fig_h_in = 7.9, 5.0, 4.0
|
|
343
|
+
else:
|
|
344
|
+
bullet_w = Inches(12.0)
|
|
345
|
+
|
|
346
|
+
bullet_box = s.shapes.add_textbox(Inches(0.7), Inches(2.4), bullet_w, Inches(4.6))
|
|
347
|
+
btf = bullet_box.text_frame; btf.word_wrap = True
|
|
348
|
+
for i, raw in enumerate(bullets):
|
|
349
|
+
p = btf.paragraphs[0] if i == 0 else btf.add_paragraph()
|
|
350
|
+
p.alignment = PP_ALIGN.LEFT
|
|
351
|
+
p.space_after = Pt(10)
|
|
352
|
+
p.line_spacing = 1.25
|
|
353
|
+
|
|
354
|
+
is_sub = raw.startswith(" ")
|
|
355
|
+
if is_sub:
|
|
356
|
+
p.level = 1
|
|
357
|
+
text = raw[2:]
|
|
358
|
+
r = p.add_run(); r.text = "— "
|
|
359
|
+
set_run(r, size=15, color=COLOR_MUTED)
|
|
360
|
+
add_styled(p, text, size=16, color=COLOR_TEXT_SUB)
|
|
361
|
+
else:
|
|
362
|
+
r = p.add_run(); r.text = "▪ "
|
|
363
|
+
set_run(r, size=14, bold=True, color=COLOR_HIGHLIGHT)
|
|
364
|
+
add_styled(p, raw, size=20, color=COLOR_TEXT)
|
|
365
|
+
|
|
366
|
+
if has_fig:
|
|
367
|
+
from PIL import Image as PILImage
|
|
368
|
+
img = PILImage.open(figure_path)
|
|
369
|
+
iw, ih = img.size
|
|
370
|
+
ar = iw / ih # width / height
|
|
371
|
+
if ar > fig_w_in / fig_h_in:
|
|
372
|
+
w_in = fig_w_in
|
|
373
|
+
h_in = fig_w_in / ar
|
|
374
|
+
else:
|
|
375
|
+
h_in = fig_h_in
|
|
376
|
+
w_in = fig_h_in * ar
|
|
377
|
+
|
|
378
|
+
fx_in = fig_x_in + (fig_w_in - w_in) / 2
|
|
379
|
+
fy_in = 2.4 + (fig_h_in - h_in) / 2
|
|
380
|
+
|
|
381
|
+
shadow = s.shapes.add_shape(MSO_SHAPE.RECTANGLE,
|
|
382
|
+
Inches(fx_in + 0.06), Inches(fy_in + 0.06),
|
|
383
|
+
Inches(w_in), Inches(h_in))
|
|
384
|
+
shadow.fill.solid(); shadow.fill.fore_color.rgb = COLOR_HAIRLINE
|
|
385
|
+
shadow.line.fill.background()
|
|
386
|
+
|
|
387
|
+
pic = s.shapes.add_picture(str(figure_path),
|
|
388
|
+
Inches(fx_in), Inches(fy_in),
|
|
389
|
+
Inches(w_in), Inches(h_in))
|
|
390
|
+
pic.line.color.rgb = COLOR_HAIRLINE
|
|
391
|
+
pic.line.width = Emu(6000)
|
|
392
|
+
|
|
393
|
+
if fig_caption:
|
|
394
|
+
cap_y_in = min(fy_in + h_in + 0.10, 6.55)
|
|
395
|
+
cap = s.shapes.add_textbox(Inches(fig_x_in), Inches(cap_y_in),
|
|
396
|
+
Inches(fig_w_in), Inches(0.6))
|
|
397
|
+
ctf = cap.text_frame; ctf.word_wrap = True
|
|
398
|
+
cp = ctf.paragraphs[0]; cp.alignment = PP_ALIGN.CENTER
|
|
399
|
+
cr = cp.add_run(); cr.text = "Figure · "
|
|
400
|
+
set_run(cr, size=10, bold=True, color=COLOR_HIGHLIGHT, letter_space="200")
|
|
401
|
+
cr2 = cp.add_run(); cr2.text = fig_caption
|
|
402
|
+
set_run(cr2, size=11, italic=True, color=COLOR_MUTED)
|
|
403
|
+
|
|
404
|
+
if footnote:
|
|
405
|
+
fn = s.shapes.add_textbox(Inches(0.7), Inches(7.05), Inches(12.0), Inches(0.35))
|
|
406
|
+
fp = fn.text_frame.paragraphs[0]; fp.alignment = PP_ALIGN.RIGHT
|
|
407
|
+
rr = fp.add_run(); rr.text = footnote
|
|
408
|
+
set_run(rr, size=10, italic=True, color=COLOR_MUTED)
|
|
409
|
+
|
|
410
|
+
if page_brand:
|
|
411
|
+
pb = s.shapes.add_textbox(Inches(0.7), Inches(7.05), Inches(4.0), Inches(0.35))
|
|
412
|
+
p = pb.text_frame.paragraphs[0]
|
|
413
|
+
r = p.add_run(); r.text = page_brand
|
|
414
|
+
set_run(r, size=9, color=COLOR_MUTED, letter_space="300")
|
|
415
|
+
|
|
416
|
+
add_notes(s, notes)
|
|
417
|
+
return s
|
|
418
|
+
|
|
419
|
+
|
|
420
|
+
def add_toc_slide(prs: Presentation, *,
|
|
421
|
+
sections: Sequence[tuple[str, str, str, str]],
|
|
422
|
+
subtitle: str = "",
|
|
423
|
+
page_brand: str | None = None,
|
|
424
|
+
notes: str | None = None):
|
|
425
|
+
"""Outline slide. `sections` = [(num, title, summary, time_label), ...].
|
|
426
|
+
|
|
427
|
+
Use num="·" for non-numbered final entry (e.g., wrap-up).
|
|
428
|
+
"""
|
|
429
|
+
s = _blank(prs)
|
|
430
|
+
|
|
431
|
+
eye = s.shapes.add_textbox(Inches(0.7), Inches(0.32), Inches(8), Inches(0.4))
|
|
432
|
+
p = eye.text_frame.paragraphs[0]
|
|
433
|
+
r = p.add_run(); r.text = "OUTLINE"
|
|
434
|
+
set_run(r, size=11, bold=True, color=COLOR_HIGHLIGHT, letter_space="400")
|
|
435
|
+
|
|
436
|
+
tb = s.shapes.add_textbox(Inches(0.7), Inches(0.8), Inches(12), Inches(1.0))
|
|
437
|
+
p = tb.text_frame.paragraphs[0]
|
|
438
|
+
r = p.add_run(); r.text = "Outline"
|
|
439
|
+
set_run(r, size=32, bold=True, color=COLOR_NAVY)
|
|
440
|
+
if subtitle:
|
|
441
|
+
p2 = tb.text_frame.add_paragraph()
|
|
442
|
+
r2 = p2.add_run(); r2.text = subtitle
|
|
443
|
+
set_run(r2, size=16, italic=True, color=COLOR_TEXT_SUB)
|
|
444
|
+
|
|
445
|
+
line = s.shapes.add_shape(MSO_SHAPE.RECTANGLE,
|
|
446
|
+
Inches(0.7), Inches(2.1), Inches(0.6), Emu(20000))
|
|
447
|
+
line.fill.solid(); line.fill.fore_color.rgb = COLOR_HIGHLIGHT
|
|
448
|
+
line.line.fill.background()
|
|
449
|
+
|
|
450
|
+
y_start = 2.5
|
|
451
|
+
row_h = 0.85
|
|
452
|
+
for i, (num, sec_title, summary, time_label) in enumerate(sections):
|
|
453
|
+
y = y_start + i * row_h
|
|
454
|
+
|
|
455
|
+
nb = s.shapes.add_textbox(Inches(0.7), Inches(y), Inches(1.0), Inches(row_h))
|
|
456
|
+
np_ = nb.text_frame.paragraphs[0]; np_.alignment = PP_ALIGN.LEFT
|
|
457
|
+
nr = np_.add_run(); nr.text = num
|
|
458
|
+
set_run(nr, size=22, bold=True,
|
|
459
|
+
color=COLOR_HIGHLIGHT if num != "·" else COLOR_MUTED)
|
|
460
|
+
|
|
461
|
+
tb2 = s.shapes.add_textbox(Inches(1.9), Inches(y), Inches(9.5), Inches(row_h))
|
|
462
|
+
tt = tb2.text_frame; tt.word_wrap = True
|
|
463
|
+
p = tt.paragraphs[0]; p.alignment = PP_ALIGN.LEFT
|
|
464
|
+
r = p.add_run(); r.text = sec_title
|
|
465
|
+
set_run(r, size=22, bold=True, color=COLOR_NAVY)
|
|
466
|
+
p.space_after = Pt(2)
|
|
467
|
+
p2 = tt.add_paragraph()
|
|
468
|
+
r2 = p2.add_run(); r2.text = summary
|
|
469
|
+
set_run(r2, size=13, color=COLOR_TEXT_SUB)
|
|
470
|
+
|
|
471
|
+
if time_label:
|
|
472
|
+
time_b = s.shapes.add_textbox(Inches(11.5), Inches(y + 0.1),
|
|
473
|
+
Inches(1.5), Inches(0.5))
|
|
474
|
+
p = time_b.text_frame.paragraphs[0]; p.alignment = PP_ALIGN.RIGHT
|
|
475
|
+
r = p.add_run(); r.text = time_label
|
|
476
|
+
set_run(r, size=12, color=COLOR_MUTED)
|
|
477
|
+
|
|
478
|
+
if i < len(sections) - 1:
|
|
479
|
+
divider = s.shapes.add_shape(MSO_SHAPE.RECTANGLE,
|
|
480
|
+
Inches(0.7), Inches(y + row_h - 0.04),
|
|
481
|
+
Inches(12.0), Emu(6000))
|
|
482
|
+
divider.fill.solid(); divider.fill.fore_color.rgb = COLOR_HAIRLINE
|
|
483
|
+
divider.line.fill.background()
|
|
484
|
+
|
|
485
|
+
if page_brand:
|
|
486
|
+
pf = s.shapes.add_textbox(Inches(0.7), Inches(7.05), Inches(12.0), Inches(0.35))
|
|
487
|
+
pp_ = pf.text_frame.paragraphs[0]
|
|
488
|
+
pr_ = pp_.add_run(); pr_.text = page_brand
|
|
489
|
+
set_run(pr_, size=9, color=COLOR_MUTED, letter_space="300")
|
|
490
|
+
|
|
491
|
+
add_notes(s, notes)
|
|
492
|
+
return s
|
|
493
|
+
|
|
494
|
+
|
|
495
|
+
def add_glossary_slide(prs: Presentation, *,
|
|
496
|
+
eyebrow: str = "KEY ABBREVIATIONS",
|
|
497
|
+
title: str = "Glossary",
|
|
498
|
+
tier1: Sequence[tuple[str, str]] = (),
|
|
499
|
+
tier2: Sequence[tuple[str, str]] = (),
|
|
500
|
+
page_brand: str | None = None,
|
|
501
|
+
notes: str | None = None):
|
|
502
|
+
"""Glossary slide for multidisciplinary audiences.
|
|
503
|
+
|
|
504
|
+
tier1: [(abbreviation, one-line context), ...] — disease/concept (4–7 items)
|
|
505
|
+
tier2: [(abbreviation, short definition), ...] — method/statistics (8–12 items, rendered 2-column)
|
|
506
|
+
|
|
507
|
+
See ~/.claude/rules/multidisciplinary-presentation.md §1.
|
|
508
|
+
"""
|
|
509
|
+
s = _blank(prs)
|
|
510
|
+
|
|
511
|
+
eye = s.shapes.add_textbox(Inches(0.7), Inches(0.32), Inches(8), Inches(0.4))
|
|
512
|
+
p = eye.text_frame.paragraphs[0]
|
|
513
|
+
r = p.add_run(); r.text = eyebrow
|
|
514
|
+
set_run(r, size=10, bold=True, color=COLOR_MUTED, letter_space="300")
|
|
515
|
+
|
|
516
|
+
tb = s.shapes.add_textbox(Inches(0.7), Inches(0.75), Inches(12.0), Inches(0.8))
|
|
517
|
+
p = tb.text_frame.paragraphs[0]
|
|
518
|
+
r = p.add_run(); r.text = title
|
|
519
|
+
set_run(r, size=30, bold=True, color=COLOR_NAVY)
|
|
520
|
+
|
|
521
|
+
line = s.shapes.add_shape(MSO_SHAPE.RECTANGLE,
|
|
522
|
+
Inches(0.7), Inches(1.65), Inches(0.6), Emu(20000))
|
|
523
|
+
line.fill.solid(); line.fill.fore_color.rgb = COLOR_HIGHLIGHT
|
|
524
|
+
line.line.fill.background()
|
|
525
|
+
|
|
526
|
+
# Tier 1 — full width
|
|
527
|
+
if tier1:
|
|
528
|
+
box = s.shapes.add_textbox(Inches(0.7), Inches(1.9), Inches(12.0), Inches(2.3))
|
|
529
|
+
tf = box.text_frame; tf.word_wrap = True
|
|
530
|
+
for i, (abbr, ctx) in enumerate(tier1):
|
|
531
|
+
p = tf.paragraphs[0] if i == 0 else tf.add_paragraph()
|
|
532
|
+
p.alignment = PP_ALIGN.LEFT
|
|
533
|
+
p.space_after = Pt(6)
|
|
534
|
+
r = p.add_run(); r.text = f"{abbr} "
|
|
535
|
+
set_run(r, size=15, bold=True, color=COLOR_NAVY)
|
|
536
|
+
r2 = p.add_run(); r2.text = ctx
|
|
537
|
+
set_run(r2, size=14, color=COLOR_TEXT_SUB)
|
|
538
|
+
|
|
539
|
+
# Tier 2 — 2-column
|
|
540
|
+
if tier2:
|
|
541
|
+
half = (len(tier2) + 1) // 2
|
|
542
|
+
for col, items in enumerate((tier2[:half], tier2[half:])):
|
|
543
|
+
x_in = 0.7 + col * 6.3
|
|
544
|
+
box = s.shapes.add_textbox(Inches(x_in), Inches(4.3),
|
|
545
|
+
Inches(6.0), Inches(2.7))
|
|
546
|
+
tf = box.text_frame; tf.word_wrap = True
|
|
547
|
+
for i, (abbr, defn) in enumerate(items):
|
|
548
|
+
p = tf.paragraphs[0] if i == 0 else tf.add_paragraph()
|
|
549
|
+
p.alignment = PP_ALIGN.LEFT
|
|
550
|
+
p.space_after = Pt(3)
|
|
551
|
+
r = p.add_run(); r.text = f"{abbr} "
|
|
552
|
+
set_run(r, size=12, bold=True, color=COLOR_NAVY)
|
|
553
|
+
r2 = p.add_run(); r2.text = defn
|
|
554
|
+
set_run(r2, size=11, color=COLOR_TEXT_SUB)
|
|
555
|
+
|
|
556
|
+
if page_brand:
|
|
557
|
+
pb = s.shapes.add_textbox(Inches(0.7), Inches(7.05), Inches(4.0), Inches(0.35))
|
|
558
|
+
p = pb.text_frame.paragraphs[0]
|
|
559
|
+
r = p.add_run(); r.text = page_brand
|
|
560
|
+
set_run(r, size=9, color=COLOR_MUTED, letter_space="300")
|
|
561
|
+
|
|
562
|
+
add_notes(s, notes)
|
|
563
|
+
return s
|
|
564
|
+
|
|
565
|
+
|
|
566
|
+
def add_closing_slide(prs: Presentation, *,
|
|
567
|
+
title: str = "Take-home messages",
|
|
568
|
+
bullets: Sequence[str] = (),
|
|
569
|
+
contact: str | None = None,
|
|
570
|
+
page_brand: str | None = None,
|
|
571
|
+
notes: str | None = None):
|
|
572
|
+
s = _blank(prs)
|
|
573
|
+
|
|
574
|
+
eye = s.shapes.add_textbox(Inches(0.7), Inches(0.32), Inches(8), Inches(0.4))
|
|
575
|
+
p = eye.text_frame.paragraphs[0]
|
|
576
|
+
r = p.add_run(); r.text = "CONCLUSION"
|
|
577
|
+
set_run(r, size=11, bold=True, color=COLOR_HIGHLIGHT, letter_space="400")
|
|
578
|
+
|
|
579
|
+
tb = s.shapes.add_textbox(Inches(0.7), Inches(0.75), Inches(12.0), Inches(0.9))
|
|
580
|
+
p = tb.text_frame.paragraphs[0]
|
|
581
|
+
r = p.add_run(); r.text = title
|
|
582
|
+
set_run(r, size=32, bold=True, color=COLOR_NAVY)
|
|
583
|
+
|
|
584
|
+
line = s.shapes.add_shape(MSO_SHAPE.RECTANGLE,
|
|
585
|
+
Inches(0.7), Inches(1.75), Inches(0.6), Emu(20000))
|
|
586
|
+
line.fill.solid(); line.fill.fore_color.rgb = COLOR_HIGHLIGHT
|
|
587
|
+
line.line.fill.background()
|
|
588
|
+
|
|
589
|
+
if bullets:
|
|
590
|
+
box = s.shapes.add_textbox(Inches(0.7), Inches(2.2), Inches(12.0), Inches(4.0))
|
|
591
|
+
tf = box.text_frame; tf.word_wrap = True
|
|
592
|
+
for i, raw in enumerate(bullets):
|
|
593
|
+
p = tf.paragraphs[0] if i == 0 else tf.add_paragraph()
|
|
594
|
+
p.alignment = PP_ALIGN.LEFT
|
|
595
|
+
p.space_after = Pt(14)
|
|
596
|
+
p.line_spacing = 1.3
|
|
597
|
+
r = p.add_run(); r.text = "▪ "
|
|
598
|
+
set_run(r, size=16, bold=True, color=COLOR_HIGHLIGHT)
|
|
599
|
+
add_styled(p, raw, size=22, color=COLOR_TEXT)
|
|
600
|
+
|
|
601
|
+
if contact:
|
|
602
|
+
cb = s.shapes.add_textbox(Inches(0.7), Inches(6.5), Inches(12.0), Inches(0.5))
|
|
603
|
+
p = cb.text_frame.paragraphs[0]; p.alignment = PP_ALIGN.LEFT
|
|
604
|
+
r = p.add_run(); r.text = contact
|
|
605
|
+
set_run(r, size=12, color=COLOR_TEXT_SUB)
|
|
606
|
+
|
|
607
|
+
if page_brand:
|
|
608
|
+
pb = s.shapes.add_textbox(Inches(0.7), Inches(7.05), Inches(4.0), Inches(0.35))
|
|
609
|
+
p = pb.text_frame.paragraphs[0]
|
|
610
|
+
r = p.add_run(); r.text = page_brand
|
|
611
|
+
set_run(r, size=9, color=COLOR_MUTED, letter_space="300")
|
|
612
|
+
|
|
613
|
+
add_notes(s, notes)
|
|
614
|
+
return s
|
|
615
|
+
|
|
616
|
+
|
|
617
|
+
# ============================================================================
|
|
618
|
+
# Mac PowerPoint compatibility — app.xml fix
|
|
619
|
+
# ============================================================================
|
|
620
|
+
|
|
621
|
+
def fix_app_xml(pptx_path: str | Path) -> None:
|
|
622
|
+
"""Patch docProps/app.xml so Mac PowerPoint stops showing the repair dialog.
|
|
623
|
+
|
|
624
|
+
Run after Presentation.save(). Updates <Slides>, <Notes>, HeadingPairs counts,
|
|
625
|
+
and TitlesOfParts vector. See ~/.claude/rules/pptx-mac-compatibility.md §5.
|
|
626
|
+
"""
|
|
627
|
+
pptx_path = Path(pptx_path)
|
|
628
|
+
prs = Presentation(pptx_path)
|
|
629
|
+
n_slides = len(prs.slides)
|
|
630
|
+
with zipfile.ZipFile(pptx_path, "r") as z:
|
|
631
|
+
n_notes = sum(
|
|
632
|
+
1 for x in z.namelist()
|
|
633
|
+
if x.startswith("ppt/notesSlides/notesSlide") and x.endswith(".xml")
|
|
634
|
+
)
|
|
635
|
+
titles: list[str] = []
|
|
636
|
+
for slide in prs.slides:
|
|
637
|
+
title = ""
|
|
638
|
+
for shape in slide.shapes:
|
|
639
|
+
if shape.has_text_frame and shape.text_frame.text.strip():
|
|
640
|
+
title = shape.text_frame.text.strip().split("\n")[0][:60]
|
|
641
|
+
break
|
|
642
|
+
titles.append(title or "Untitled")
|
|
643
|
+
|
|
644
|
+
esc = lambda t: t.replace("&", "&").replace("<", "<").replace(">", ">")
|
|
645
|
+
title_items = "".join(f"<vt:lpstr>{esc(t)}</vt:lpstr>" for t in titles)
|
|
646
|
+
new_app_xml = (
|
|
647
|
+
'<?xml version="1.0" encoding="UTF-8" standalone="yes"?>'
|
|
648
|
+
'<Properties xmlns="http://schemas.openxmlformats.org/officeDocument/2006/extended-properties" '
|
|
649
|
+
'xmlns:vt="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes">'
|
|
650
|
+
'<TotalTime>1</TotalTime><Words>0</Words>'
|
|
651
|
+
'<Application>Microsoft Macintosh PowerPoint</Application>'
|
|
652
|
+
'<PresentationFormat>Widescreen</PresentationFormat><Paragraphs>0</Paragraphs>'
|
|
653
|
+
f'<Slides>{n_slides}</Slides><Notes>{n_notes}</Notes>'
|
|
654
|
+
'<HiddenSlides>0</HiddenSlides><MMClips>0</MMClips><ScaleCrop>false</ScaleCrop>'
|
|
655
|
+
'<HeadingPairs><vt:vector size="4" baseType="variant">'
|
|
656
|
+
'<vt:variant><vt:lpstr>Theme</vt:lpstr></vt:variant>'
|
|
657
|
+
'<vt:variant><vt:i4>1</vt:i4></vt:variant>'
|
|
658
|
+
'<vt:variant><vt:lpstr>Slide Titles</vt:lpstr></vt:variant>'
|
|
659
|
+
f'<vt:variant><vt:i4>{n_slides}</vt:i4></vt:variant>'
|
|
660
|
+
'</vt:vector></HeadingPairs>'
|
|
661
|
+
f'<TitlesOfParts><vt:vector size="{n_slides + 1}" baseType="lpstr">'
|
|
662
|
+
f'<vt:lpstr>Office Theme</vt:lpstr>{title_items}'
|
|
663
|
+
'</vt:vector></TitlesOfParts>'
|
|
664
|
+
'<Manager></Manager><Company></Company><LinksUpToDate>false</LinksUpToDate>'
|
|
665
|
+
'<SharedDoc>false</SharedDoc><HyperlinkBase></HyperlinkBase>'
|
|
666
|
+
'<HyperlinksChanged>false</HyperlinksChanged><AppVersion>14.0000</AppVersion>'
|
|
667
|
+
'</Properties>'
|
|
668
|
+
)
|
|
669
|
+
tmp = pptx_path.with_suffix(".tmp.pptx")
|
|
670
|
+
with zipfile.ZipFile(pptx_path, "r") as zin, \
|
|
671
|
+
zipfile.ZipFile(tmp, "w", zipfile.ZIP_DEFLATED) as zout:
|
|
672
|
+
for item in zin.namelist():
|
|
673
|
+
zout.writestr(item, new_app_xml if item == "docProps/app.xml" else zin.read(item))
|
|
674
|
+
shutil.move(tmp, pptx_path)
|
|
675
|
+
print(f"app.xml patched: Slides={n_slides}, Notes={n_notes}")
|
|
676
|
+
|
|
677
|
+
|
|
678
|
+
__all__ = [
|
|
679
|
+
"new_presentation",
|
|
680
|
+
"add_title_slide", "add_toc_slide", "add_section_divider",
|
|
681
|
+
"add_transition_slide", "add_content_slide",
|
|
682
|
+
"add_glossary_slide", "add_closing_slide",
|
|
683
|
+
"set_run", "add_styled", "add_notes",
|
|
684
|
+
"fix_app_xml",
|
|
685
|
+
"COLOR_NAVY", "COLOR_HIGHLIGHT", "COLOR_TEXT", "COLOR_TEXT_SUB",
|
|
686
|
+
"COLOR_MUTED", "COLOR_HAIRLINE", "COLOR_WHITE", "COLOR_DIVIDER_BG",
|
|
687
|
+
"FONT_KR", "FONT_EN",
|
|
688
|
+
]
|