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
- package/skills/write-paper/references/journal_profiles/AJR.md +149 -0
- 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
- package/skills/write-paper/references/journal_profiles/CVIR.md +157 -0
- package/skills/write-paper/references/journal_profiles/Chest.md +270 -0
- package/skills/write-paper/references/journal_profiles/Clinical_Radiology.md +160 -0
- 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
- package/skills/write-paper/references/journal_profiles/Hepatology_International.md +106 -0
- package/skills/write-paper/references/journal_profiles/IEEE_TMI.md +180 -0
- package/skills/write-paper/references/journal_profiles/INSI.md +163 -0
- package/skills/write-paper/references/journal_profiles/Investigative_Radiology.md +86 -0
- package/skills/write-paper/references/journal_profiles/JACC_Advances.md +197 -0
- package/skills/write-paper/references/journal_profiles/JACC_Asia.md +168 -0
- package/skills/write-paper/references/journal_profiles/JACR.md +87 -0
- package/skills/write-paper/references/journal_profiles/JAMA.md +188 -0
- package/skills/write-paper/references/journal_profiles/JAMA_Network_Open.md +170 -0
- package/skills/write-paper/references/journal_profiles/JCSM.md +266 -0
- package/skills/write-paper/references/journal_profiles/JKMS.md +201 -0
- package/skills/write-paper/references/journal_profiles/JMIR.md +88 -0
- package/skills/write-paper/references/journal_profiles/JMIR_Medical_Education.md +86 -0
- package/skills/write-paper/references/journal_profiles/JNIS.md +227 -0
- package/skills/write-paper/references/journal_profiles/JVIR.md +158 -0
- package/skills/write-paper/references/journal_profiles/Journal_of_Clinical_Endocrinology_and_Metabolism.md +191 -0
- package/skills/write-paper/references/journal_profiles/Journal_of_Stroke.md +176 -0
- package/skills/write-paper/references/journal_profiles/KJR.md +185 -0
- package/skills/write-paper/references/journal_profiles/Korean_Circulation_Journal.md +184 -0
- package/skills/write-paper/references/journal_profiles/Korean_Journal_of_Internal_Medicine.md +178 -0
- package/skills/write-paper/references/journal_profiles/Lancet_Gastroenterology_and_Hepatology.md +127 -0
- package/skills/write-paper/references/journal_profiles/Liver_International.md +165 -0
- package/skills/write-paper/references/journal_profiles/Medical_Image_Analysis.md +147 -0
- package/skills/write-paper/references/journal_profiles/NEJM.md +147 -0
- package/skills/write-paper/references/journal_profiles/Nature_Medicine.md +181 -0
- package/skills/write-paper/references/journal_profiles/Neuroradiology.md +151 -0
- package/skills/write-paper/references/journal_profiles/Nutrition_Metabolism_and_Cardiovascular_Diseases.md +184 -0
- package/skills/write-paper/references/journal_profiles/PLOS_Medicine.md +166 -0
- package/skills/write-paper/references/journal_profiles/RYAI.md +124 -0
- package/skills/write-paper/references/journal_profiles/Radiology.md +173 -0
- package/skills/write-paper/references/journal_profiles/Skeletal_Radiology.md +135 -0
- package/skills/write-paper/references/journal_profiles/Stroke.md +210 -0
- package/skills/write-paper/references/journal_profiles/The_BMJ.md +121 -0
- package/skills/write-paper/references/journal_profiles/The_Lancet.md +112 -0
- package/skills/write-paper/references/journal_profiles/The_Lancet_Digital_Health.md +104 -0
- 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
- package/skills/write-paper/references/paper_types/ai_validation.md +270 -0
- package/skills/write-paper/references/paper_types/animal_study.md +194 -0
- package/skills/write-paper/references/paper_types/case_report.md +237 -0
- package/skills/write-paper/references/paper_types/cross_national.md +328 -0
- package/skills/write-paper/references/paper_types/letter.md +127 -0
- package/skills/write-paper/references/paper_types/meta_analysis.md +181 -0
- package/skills/write-paper/references/paper_types/nhis_cohort.md +297 -0
- package/skills/write-paper/references/paper_types/original_article.md +221 -0
- package/skills/write-paper/references/paper_types/technical_note.md +131 -0
- package/skills/write-paper/references/section_guides/discussion.md +155 -0
- package/skills/write-paper/references/section_guides/introduction.md +108 -0
- package/skills/write-paper/references/section_guides/methods.md +144 -0
- package/skills/write-paper/references/section_guides/results.md +113 -0
- package/skills/write-paper/references/section_guides/step7_1_classical_qc.md +67 -0
- package/skills/write-paper/references/section_guides/step7_4a_audit_recovery.md +74 -0
- package/skills/write-paper/references/section_guides/title_abstract.md +123 -0
- package/skills/write-paper/references/section_templates/methods_statistical.md +147 -0
- package/skills/write-paper/scripts/check_placeholders.py +182 -0
- package/skills/write-paper/skill.yml +48 -0
- package/skills/write-paper/tests/test_placeholders.sh +107 -0
- package/skills/write-protocol/SKILL.md +243 -0
- package/skills/write-protocol/references/ethics_checklist.md +150 -0
- package/skills/write-protocol/references/protocol_template.md +304 -0
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#!/usr/bin/env bash
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# Regression test for the multi-copy manuscript divergence detector (Phase 8).
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# Synthetic fixtures: an SSOT and two copies — one reworded but claim-complete
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# (OK), one missing an SSOT claim (p = 0.074, an unpropagated edit). Stdlib-only.
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set -u
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HERE="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
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SCRIPT="$HERE/../scripts/detect_copy_divergence.py"
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SSOT="$HERE/fixtures/ssot.md"
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OKC="$HERE/fixtures/copy_ok.md"
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STALE="$HERE/fixtures/copy_stale.md"
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OUT="$(mktemp -t cd_XXXX).json"
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trap 'rm -f "$OUT"' EXIT
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fail=0
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check() { local label="$1"; shift
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if "$@" >/dev/null 2>&1; then printf ' PASS %s\n' "$label"
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else printf ' FAIL %s\n' "$label"; fail=$((fail+1)); fi
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}
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[[ -f "$SCRIPT" ]] || { echo "ENV-ERR: script missing" >&2; exit 2; }
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# OK copy alone -> exit 0.
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python3 "$SCRIPT" --ssot "$SSOT" --copy "$OKC" --strict >/dev/null 2>&1
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check "exit 0 when the copy carries every SSOT claim" test "$?" -eq 0
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# Stale copy -> exit 1, flags the unpropagated claim.
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python3 "$SCRIPT" --ssot "$SSOT" --copy "$OKC" --copy "$STALE" --out "$OUT" --strict >/dev/null 2>&1
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check "exit 1 when a copy is missing an SSOT claim" test "$?" -eq 1
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check "verdict DIVERGENT" python3 -c "
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import json; assert json.load(open('$OUT'))['verdict']=='DIVERGENT'"
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check "stale copy flags the unpropagated p-value" python3 -c "
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import json
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d=json.load(open('$OUT'))
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stale=[c for c in d['copies'] if c['verdict']=='STALE_COPY']
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assert stale and any('p=0.074' in u for u in stale[0]['unpropagated_to_copy'])"
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check "OK copy not flagged" python3 -c "
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import json
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d=json.load(open('$OUT'))
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ok=[c for c in d['copies'] if c['copy'].endswith('copy_ok.md')]
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assert ok and ok[0]['verdict']=='OK'"
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echo "fail=$fail"; [[ "$fail" -eq 0 ]] && echo "ALL PASS" || echo "FAILURES: $fail"
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#!/usr/bin/env bash
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# Test scripts/check_cross_artifact_stale.py — the A3 cross-artifact staleness gate.
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# Synthetic, PII-free fixtures: a body that corrects two labeled values, a stale
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# supplement that disagrees, a checklist built against an older manuscript version,
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# and a clean supplement that agrees.
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set -u
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HERE="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
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SCRIPT="$HERE/../scripts/check_cross_artifact_stale.py"
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PASS=0
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FAIL=0
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ok() { echo " PASS: $1"; PASS=$((PASS+1)); }
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bad() { echo " FAIL: $1"; FAIL=$((FAIL+1)); }
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WORK="$(mktemp -d)"
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trap 'rm -rf "$WORK"' EXIT
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# body (v8 in filename) — corrected values
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cat > "$WORK/manuscript_v8.md" <<'EOF'
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## Results
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The complete-case analysis included 95.7% of the cohort.
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Inter-rater agreement was substantial (kappa = 0.923).
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EOF
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# stale supplement: disagreeing values for the same labels
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mkdir -p "$WORK/aux"
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cat > "$WORK/aux/supplement.md" <<'EOF'
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Footnote: complete-case retention was 7.5% after exclusions.
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Reliability sub-analysis: kappa = 0.904.
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EOF
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# checklist built against an older manuscript version
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cat > "$WORK/aux/strobe_checklist.md" <<'EOF'
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Target manuscript: cohort study v6 (2026-04-20)
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Item 13: see Results, line 42.
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EOF
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# clean supplement that agrees with the body
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mkdir -p "$WORK/clean"
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cat > "$WORK/clean/supplement.md" <<'EOF'
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Footnote: complete-case retention was 95.7%.
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Reliability: kappa = 0.923.
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EOF
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run() { python3 "$SCRIPT" "$@" 2>/dev/null; }
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# 1. drift + version-stale -> exit 1
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run --manuscript "$WORK/manuscript_v8.md" --aux "$WORK/aux" --quiet
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[ $? -eq 1 ] && ok "stale aux + old checklist version -> exit 1" || bad "should fail"
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# 2. JSON reports both finding types
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run --manuscript "$WORK/manuscript_v8.md" --aux "$WORK/aux" --out "$WORK/r.json" --quiet
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python3 -c "
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import json,sys
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d=json.load(open('$WORK/r.json'))
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types={f['type'] for f in d['findings']}
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sys.exit(0 if {'labeled_value_drift','checklist_version_stale'} <= types
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and d['summary']['stale'] >= 2 and d['summary']['version_stale'] >= 1 else 1)
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" && ok "JSON: labeled_value_drift (kappa+complete_case) + version_stale" || bad "JSON findings incomplete"
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# 3. explicit --manuscript-version overrides filename inference
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run --manuscript "$WORK/manuscript_v8.md" --aux "$WORK/aux/strobe_checklist.md" \
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--manuscript-version v8 --out "$WORK/r2.json" --quiet
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python3 -c "
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import json,sys
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d=json.load(open('$WORK/r2.json'))
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sys.exit(0 if d['summary']['version_stale'] == 1 else 1)
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" && ok "explicit --manuscript-version flags stale checklist" || bad "version flag failed"
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# 4. clean supplement that agrees -> exit 0
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run --manuscript "$WORK/manuscript_v8.md" --aux "$WORK/clean" --quiet
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[ $? -eq 0 ] && ok "agreeing supplement passes" || bad "agreeing supplement should pass"
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74
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# 5. missing --aux -> usage error (exit 2)
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run --manuscript "$WORK/manuscript_v8.md" --quiet
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[ $? -eq 2 ] && ok "missing --aux -> exit 2" || bad "missing --aux should be usage error"
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echo ""
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echo "test_cross_artifact_stale: $PASS passed, $FAIL failed"
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[ "$FAIL" -eq 0 ]
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@@ -0,0 +1,132 @@
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#!/usr/bin/env bash
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# Regression tests for sync-submission cross_document_n_check.py.
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#
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4
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# Synthetic fixtures only (no project paths, no manuscript IDs).
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# Skip with NETWORK=0 — this script does not use the network.
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#
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7
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# Usage:
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# skills/sync-submission/tests/test_cross_document_n.sh
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# Exit codes:
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10
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# 0 — all tests passed
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# 1 — at least one test regressed
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# 2 — environment problem
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set -uo pipefail
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REPO_ROOT="$(cd "$(dirname "$0")/../../.." && pwd)"
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SCRIPT="$REPO_ROOT/skills/sync-submission/scripts/cross_document_n_check.py"
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TMP="$(mktemp -d -t cross_doc_n.XXXXXX)"
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trap 'rm -rf "$TMP"' EXIT
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if [[ ! -f "$SCRIPT" ]]; then
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echo "ENV-ERR: script not found at $SCRIPT" >&2
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exit 2
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fi
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command -v python3 >/dev/null 2>&1 || { echo "ENV-ERR: python3 missing" >&2; exit 2; }
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fail=0
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ran=0
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|
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30
|
+
assert_exit() {
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|
31
|
+
local label="$1" expected="$2" actual="$3"
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|
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|
+
ran=$((ran + 1))
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|
33
|
+
if [[ "$expected" == "$actual" ]]; then
|
|
34
|
+
printf ' PASS %-50s exit=%s\n' "$label" "$actual"
|
|
35
|
+
else
|
|
36
|
+
printf ' FAIL %-50s expected=%s actual=%s\n' "$label" "$expected" "$actual"
|
|
37
|
+
fail=$((fail + 1))
|
|
38
|
+
fi
|
|
39
|
+
}
|
|
40
|
+
|
|
41
|
+
# --------------------------------------------------------------------------
|
|
42
|
+
# Case 1: two documents agreeing on N. Should PASS (exit 0).
|
|
43
|
+
# --------------------------------------------------------------------------
|
|
44
|
+
PROJ1="$TMP/case1_consistent"
|
|
45
|
+
mkdir -p "$PROJ1"
|
|
46
|
+
cat > "$PROJ1/abstract.md" <<'EOF'
|
|
47
|
+
We included 42 studies after screening.
|
|
48
|
+
EOF
|
|
49
|
+
cat > "$PROJ1/manuscript.md" <<'EOF'
|
|
50
|
+
Results section. Across 42 included studies, the pooled estimate was...
|
|
51
|
+
EOF
|
|
52
|
+
python3 "$SCRIPT" --root "$PROJ1" --out "$PROJ1/qc/n.json" --quiet
|
|
53
|
+
assert_exit "case 1: consistent N (42 = 42)" 0 $?
|
|
54
|
+
|
|
55
|
+
# --------------------------------------------------------------------------
|
|
56
|
+
# Case 2: drift. Should FAIL (exit 1).
|
|
57
|
+
# --------------------------------------------------------------------------
|
|
58
|
+
PROJ2="$TMP/case2_drift"
|
|
59
|
+
mkdir -p "$PROJ2"
|
|
60
|
+
cat > "$PROJ2/abstract.md" <<'EOF'
|
|
61
|
+
We included 63 studies after dual-reviewer screening.
|
|
62
|
+
EOF
|
|
63
|
+
cat > "$PROJ2/manuscript.md" <<'EOF'
|
|
64
|
+
A total of 64 included studies were extracted for synthesis.
|
|
65
|
+
EOF
|
|
66
|
+
python3 "$SCRIPT" --root "$PROJ2" --out "$PROJ2/qc/n.json" --quiet
|
|
67
|
+
assert_exit "case 2: drift (63 vs 64)" 1 $?
|
|
68
|
+
# Verify the JSON content is well-formed and flags the right category.
|
|
69
|
+
python3 - "$PROJ2/qc/n.json" <<'PY' || fail=$((fail + 1))
|
|
70
|
+
import json, sys
|
|
71
|
+
with open(sys.argv[1]) as fh:
|
|
72
|
+
rep = json.load(fh)
|
|
73
|
+
assert rep["submission_safe"] is False, rep
|
|
74
|
+
assert rep["drift_count"] == 1, rep
|
|
75
|
+
assert rep["drifts"][0]["category"] == "included", rep
|
|
76
|
+
vs = set(rep["drifts"][0]["values"])
|
|
77
|
+
assert vs == {63, 64}, rep
|
|
78
|
+
PY
|
|
79
|
+
|
|
80
|
+
# --------------------------------------------------------------------------
|
|
81
|
+
# Case 3: pool-lock mismatch.
|
|
82
|
+
# --------------------------------------------------------------------------
|
|
83
|
+
if python3 -c "import yaml" 2>/dev/null; then
|
|
84
|
+
PROJ3="$TMP/case3_lock"
|
|
85
|
+
mkdir -p "$PROJ3"
|
|
86
|
+
cat > "$PROJ3/abstract.md" <<'EOF'
|
|
87
|
+
We included 50 studies after screening.
|
|
88
|
+
EOF
|
|
89
|
+
cat > "$PROJ3/manuscript.md" <<'EOF'
|
|
90
|
+
Across 50 included studies, the pooled estimate was ...
|
|
91
|
+
EOF
|
|
92
|
+
cat > "$PROJ3/lock.yaml" <<'EOF'
|
|
93
|
+
freeze_date: 2026-01-01
|
|
94
|
+
final_pool_n: 48
|
|
95
|
+
include_count: 48
|
|
96
|
+
exclude_count: 100
|
|
97
|
+
EOF
|
|
98
|
+
python3 "$SCRIPT" --root "$PROJ3" --pool-lock "$PROJ3/lock.yaml" \
|
|
99
|
+
--out "$PROJ3/qc/n.json" --quiet
|
|
100
|
+
assert_exit "case 3: pool-lock mismatch (50 vs locked 48)" 1 $?
|
|
101
|
+
python3 - "$PROJ3/qc/n.json" <<'PY' || fail=$((fail + 1))
|
|
102
|
+
import json, sys
|
|
103
|
+
with open(sys.argv[1]) as fh:
|
|
104
|
+
rep = json.load(fh)
|
|
105
|
+
assert rep["lock_violations"], rep
|
|
106
|
+
v = rep["lock_violations"][0]
|
|
107
|
+
assert v["violation"] == "pool-lock-mismatch", v
|
|
108
|
+
assert v["expected"] == 48, v
|
|
109
|
+
assert v["actual"] == 50, v
|
|
110
|
+
PY
|
|
111
|
+
else
|
|
112
|
+
printf ' SKIP %-50s reason=pyyaml unavailable\n' "case 3: pool-lock"
|
|
113
|
+
fi
|
|
114
|
+
|
|
115
|
+
# --------------------------------------------------------------------------
|
|
116
|
+
# Case 4: explicit --files. Should also work.
|
|
117
|
+
# --------------------------------------------------------------------------
|
|
118
|
+
PROJ4="$TMP/case4_files"
|
|
119
|
+
mkdir -p "$PROJ4/sub"
|
|
120
|
+
cat > "$PROJ4/sub/a.md" <<'EOF'
|
|
121
|
+
We included 30 patients in the analysis.
|
|
122
|
+
EOF
|
|
123
|
+
cat > "$PROJ4/sub/b.md" <<'EOF'
|
|
124
|
+
30 patients were enrolled.
|
|
125
|
+
EOF
|
|
126
|
+
python3 "$SCRIPT" --files "$PROJ4/sub/a.md" "$PROJ4/sub/b.md" \
|
|
127
|
+
--out "$PROJ4/qc/n.json" --quiet
|
|
128
|
+
assert_exit "case 4: explicit --files PASS (30 = 30)" 0 $?
|
|
129
|
+
|
|
130
|
+
echo ""
|
|
131
|
+
echo "ran=$ran fail=$fail"
|
|
132
|
+
[[ $fail -eq 0 ]]
|
|
@@ -0,0 +1,112 @@
|
|
|
1
|
+
#!/usr/bin/env bash
|
|
2
|
+
# Test scripts/preflight_gate.py — the A6 submission pre-flight orchestrator.
|
|
3
|
+
# Builds synthetic, PII-free fixture projects in a temp dir and asserts the gate
|
|
4
|
+
# halts on a deterministic blocker, passes a clean package, tolerates absent
|
|
5
|
+
# inputs (skipped, not blocker), normalizes the inverted cover_letter exit code,
|
|
6
|
+
# and honors --require / --skip. Stdlib-only; offline (no network).
|
|
7
|
+
set -u
|
|
8
|
+
|
|
9
|
+
HERE="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
|
|
10
|
+
SCRIPT="$HERE/../scripts/preflight_gate.py"
|
|
11
|
+
PASS=0
|
|
12
|
+
FAIL=0
|
|
13
|
+
ok() { echo " PASS: $1"; PASS=$((PASS+1)); }
|
|
14
|
+
bad() { echo " FAIL: $1"; FAIL=$((FAIL+1)); }
|
|
15
|
+
|
|
16
|
+
WORK="$(mktemp -d)"
|
|
17
|
+
trap 'rm -rf "$WORK"' EXIT
|
|
18
|
+
|
|
19
|
+
DIRTY="$WORK/dirty"
|
|
20
|
+
CLEAN="$WORK/clean"
|
|
21
|
+
mkdir -p "$DIRTY/manuscript" "$CLEAN/manuscript" "$CLEAN/submission/chest/manuscript"
|
|
22
|
+
|
|
23
|
+
# dirty: an unresolved [@NEW:] placeholder + a TODO; bib does not define the marker
|
|
24
|
+
cat > "$DIRTY/manuscript/manuscript.md" <<'EOF'
|
|
25
|
+
# Introduction
|
|
26
|
+
|
|
27
|
+
We follow prior work [@smith2020] and a competing-risk model [@NEW:competing-risk].
|
|
28
|
+
|
|
29
|
+
## Methods
|
|
30
|
+
|
|
31
|
+
Analysis used R. TODO: cite the package.
|
|
32
|
+
|
|
33
|
+
## References
|
|
34
|
+
EOF
|
|
35
|
+
cat > "$DIRTY/refs.bib" <<'EOF'
|
|
36
|
+
@article{smith2020, title={A real paper}, author={Smith, John}, journal={NEJM}, year={2020}, doi={10.1056/x}}
|
|
37
|
+
EOF
|
|
38
|
+
|
|
39
|
+
# clean: no markers, every cited key defined
|
|
40
|
+
cat > "$CLEAN/manuscript/manuscript.md" <<'EOF'
|
|
41
|
+
# Introduction
|
|
42
|
+
|
|
43
|
+
We follow prior work [@smith2020] using a competing-risk model.
|
|
44
|
+
|
|
45
|
+
## Methods
|
|
46
|
+
|
|
47
|
+
Analysis used R version 4.3.
|
|
48
|
+
|
|
49
|
+
## References
|
|
50
|
+
EOF
|
|
51
|
+
cat > "$CLEAN/refs.bib" <<'EOF'
|
|
52
|
+
@article{smith2020, title={A real paper}, author={Smith, John}, journal={NEJM}, year={2020}, doi={10.1056/x}}
|
|
53
|
+
EOF
|
|
54
|
+
|
|
55
|
+
J() { python3 -c "import json,sys; d=json.load(open(sys.argv[1])); print(d[sys.argv[2]] if sys.argv[2] in d else json.dumps(d))" "$@"; }
|
|
56
|
+
STATUS() { python3 -c "import json,sys; d=json.load(open(sys.argv[1])); c=[x for x in d['checks'] if x['id']==sys.argv[2]][0]; print(c['status'])" "$@"; }
|
|
57
|
+
|
|
58
|
+
# 1. dirty halts with exit 1
|
|
59
|
+
python3 "$SCRIPT" --project-root "$DIRTY" --quiet
|
|
60
|
+
[ $? -eq 1 ] && ok "dirty package halts (exit 1)" || bad "dirty package should halt"
|
|
61
|
+
|
|
62
|
+
# 2. report: halt true, placeholders blocker, absent inputs skipped (tolerance)
|
|
63
|
+
RPT="$DIRTY/qc/preflight_gate_report.json"
|
|
64
|
+
[ "$(J "$RPT" halt)" = "True" ] && ok "report halt=true" || bad "report halt should be true"
|
|
65
|
+
[ "$(STATUS "$RPT" placeholders)" = "blocker" ] && ok "placeholders is a blocker" || bad "placeholders should block"
|
|
66
|
+
[ "$(STATUS "$RPT" cover_letter_drift)" = "skipped" ] && ok "cover_letter_drift skipped (no cover letter)" || bad "cover_letter_drift should skip"
|
|
67
|
+
[ "$(STATUS "$RPT" copy_divergence)" = "skipped" ] && ok "copy_divergence skipped (no copies)" || bad "copy_divergence should skip"
|
|
68
|
+
[ "$(STATUS "$RPT" sync_drift)" = "skipped" ] && ok "sync_drift skipped (no journal)" || bad "sync_drift should skip"
|
|
69
|
+
|
|
70
|
+
# 3. references is a P1 warn (offline unverified), never a blocker by itself
|
|
71
|
+
[ "$(STATUS "$RPT" references)" = "warn" ] && ok "references offline -> warn (non-halting)" || bad "references should warn offline"
|
|
72
|
+
|
|
73
|
+
# 4. clean package passes (exit 0)
|
|
74
|
+
python3 "$SCRIPT" --project-root "$CLEAN" --quiet
|
|
75
|
+
[ $? -eq 0 ] && ok "clean package passes (exit 0)" || bad "clean package should pass"
|
|
76
|
+
[ "$(J "$CLEAN/qc/preflight_gate_report.json" submission_safe)" = "True" ] && ok "clean report submission_safe=true" || bad "clean should be submission_safe"
|
|
77
|
+
|
|
78
|
+
# 5. inverted cover-letter exit code normalized to warn (default), blocker under --require
|
|
79
|
+
cat > "$CLEAN/submission/chest/cover_letter.md" <<'EOF'
|
|
80
|
+
Dear Editor, the manuscript is approximately 8000 words with 99 references. Sincerely,
|
|
81
|
+
EOF
|
|
82
|
+
python3 "$SCRIPT" --project-root "$CLEAN" --journal chest --quiet
|
|
83
|
+
[ $? -eq 0 ] && ok "cover-letter drift warns (P1, non-halting by default)" || bad "cover drift should not halt by default"
|
|
84
|
+
RC="$CLEAN/qc/preflight_gate_report.json"
|
|
85
|
+
python3 -c "
|
|
86
|
+
import json,sys
|
|
87
|
+
d=json.load(open('$RC')); c=[x for x in d['checks'] if x['id']=='cover_letter_drift'][0]
|
|
88
|
+
sys.exit(0 if c['exit_code']==2 and c['status']=='warn' else 1)
|
|
89
|
+
" && ok "cover_letter inverted exit 2 normalized to warn" || bad "cover_letter exit normalization wrong"
|
|
90
|
+
|
|
91
|
+
python3 "$SCRIPT" --project-root "$CLEAN" --journal chest --require cover_letter_drift --quiet
|
|
92
|
+
[ $? -eq 1 ] && ok "--require cover_letter_drift promotes to blocker (halt)" || bad "--require should halt on cover drift"
|
|
93
|
+
|
|
94
|
+
# 6. --strict promotes all P1 to halting (cover drift now blocks)
|
|
95
|
+
python3 "$SCRIPT" --project-root "$CLEAN" --journal chest --strict --quiet
|
|
96
|
+
[ $? -eq 1 ] && ok "--strict promotes P1 cover drift to halt" || bad "--strict should halt on cover drift"
|
|
97
|
+
|
|
98
|
+
# 7. --skip removes a check
|
|
99
|
+
python3 "$SCRIPT" --project-root "$CLEAN" --journal chest --strict --skip cover_letter_drift --quiet
|
|
100
|
+
[ $? -eq 0 ] && ok "--skip cover_letter_drift drops it (clean pass under --strict)" || bad "--skip should drop the check"
|
|
101
|
+
|
|
102
|
+
# 8. --require on a check that cannot run -> gate error (exit 2)
|
|
103
|
+
python3 "$SCRIPT" --project-root "$DIRTY" --require sync_drift --quiet
|
|
104
|
+
[ $? -eq 2 ] && ok "--require sync_drift (no journal) -> gate error exit 2" || bad "required-but-unrunnable should exit 2"
|
|
105
|
+
|
|
106
|
+
# 9. unknown check id -> exit 2
|
|
107
|
+
python3 "$SCRIPT" --project-root "$CLEAN" --require nonsense --quiet 2>/dev/null
|
|
108
|
+
[ $? -eq 2 ] && ok "unknown --require id -> exit 2" || bad "unknown id should exit 2"
|
|
109
|
+
|
|
110
|
+
echo ""
|
|
111
|
+
echo "test_preflight_gate: $PASS passed, $FAIL failed"
|
|
112
|
+
[ "$FAIL" -eq 0 ]
|
|
@@ -0,0 +1,122 @@
|
|
|
1
|
+
#!/usr/bin/env bash
|
|
2
|
+
# Regression tests for sync-submission scope_drift_check.py.
|
|
3
|
+
#
|
|
4
|
+
# Synthetic fixtures only. No network needed.
|
|
5
|
+
|
|
6
|
+
set -uo pipefail
|
|
7
|
+
|
|
8
|
+
REPO_ROOT="$(cd "$(dirname "$0")/../../.." && pwd)"
|
|
9
|
+
SCRIPT="$REPO_ROOT/skills/sync-submission/scripts/scope_drift_check.py"
|
|
10
|
+
TMP="$(mktemp -d -t scope_drift.XXXXXX)"
|
|
11
|
+
trap 'rm -rf "$TMP"' EXIT
|
|
12
|
+
|
|
13
|
+
[[ -f "$SCRIPT" ]] || { echo "ENV-ERR: script missing" >&2; exit 2; }
|
|
14
|
+
command -v python3 >/dev/null 2>&1 || { echo "ENV-ERR: python3 missing" >&2; exit 2; }
|
|
15
|
+
|
|
16
|
+
fail=0
|
|
17
|
+
ran=0
|
|
18
|
+
assert_exit() {
|
|
19
|
+
local label="$1" expected="$2" actual="$3"
|
|
20
|
+
ran=$((ran + 1))
|
|
21
|
+
if [[ "$expected" == "$actual" ]]; then
|
|
22
|
+
printf ' PASS %-50s exit=%s\n' "$label" "$actual"
|
|
23
|
+
else
|
|
24
|
+
printf ' FAIL %-50s expected=%s actual=%s\n' "$label" "$expected" "$actual"
|
|
25
|
+
fail=$((fail + 1))
|
|
26
|
+
fi
|
|
27
|
+
}
|
|
28
|
+
|
|
29
|
+
# --------------------------------------------------------------------------
|
|
30
|
+
# Case 1: well-formed manuscript. AUC appears in Methods, Results, Limitations.
|
|
31
|
+
# --------------------------------------------------------------------------
|
|
32
|
+
MS1="$TMP/case1.md"
|
|
33
|
+
cat > "$MS1" <<'EOF'
|
|
34
|
+
## **METHODS**
|
|
35
|
+
We computed the area under the curve (AUC) on the held-out test set. The
|
|
36
|
+
primary metric is AUC = 0.820.
|
|
37
|
+
|
|
38
|
+
## **RESULTS**
|
|
39
|
+
The pooled AUC was 0.820 (95% CI 0.78 to 0.86).
|
|
40
|
+
|
|
41
|
+
## **DISCUSSION**
|
|
42
|
+
|
|
43
|
+
### Limitations
|
|
44
|
+
A sensitivity analysis on the primary AUC of 0.820 was not pre-specified.
|
|
45
|
+
EOF
|
|
46
|
+
python3 "$SCRIPT" --manuscript "$MS1" --out "$TMP/case1.json" --quiet
|
|
47
|
+
assert_exit "case 1: consistent anchor (0.820 in all)" 0 $?
|
|
48
|
+
|
|
49
|
+
# --------------------------------------------------------------------------
|
|
50
|
+
# Case 2: AUC 0.869 appears only in Limitations. Should FAIL.
|
|
51
|
+
# --------------------------------------------------------------------------
|
|
52
|
+
MS2="$TMP/case2.md"
|
|
53
|
+
cat > "$MS2" <<'EOF'
|
|
54
|
+
## **METHODS**
|
|
55
|
+
We computed AUC on the held-out test set.
|
|
56
|
+
|
|
57
|
+
## **RESULTS**
|
|
58
|
+
The pooled AUC was 0.820 (95% CI 0.78 to 0.86).
|
|
59
|
+
|
|
60
|
+
## **DISCUSSION**
|
|
61
|
+
|
|
62
|
+
### Limitations
|
|
63
|
+
A leave-pair-out sensitivity analysis produced an envelope of AUC values:
|
|
64
|
+
primary pool of 0.869 (95% CI 0.81 to 0.92), with neighborhood values
|
|
65
|
+
0.851, 0.872, 0.881, and 0.890.
|
|
66
|
+
EOF
|
|
67
|
+
python3 "$SCRIPT" --manuscript "$MS2" --out "$TMP/case2.json" --quiet
|
|
68
|
+
assert_exit "case 2: 0.869 limits-only anchor" 1 $?
|
|
69
|
+
python3 - "$TMP/case2.json" <<'PY' || fail=$((fail + 1))
|
|
70
|
+
import json, sys
|
|
71
|
+
with open(sys.argv[1]) as fh: rep = json.load(fh)
|
|
72
|
+
anchors = [a["anchor"] for a in rep["limitations_only_anchors"]]
|
|
73
|
+
assert "0.869" in anchors, anchors
|
|
74
|
+
PY
|
|
75
|
+
|
|
76
|
+
# --------------------------------------------------------------------------
|
|
77
|
+
# Case 3: PROSPERO commits to Freeman-Tukey but Methods does not.
|
|
78
|
+
# --------------------------------------------------------------------------
|
|
79
|
+
MS3="$TMP/case3.md"
|
|
80
|
+
PR3="$TMP/case3_prospero.md"
|
|
81
|
+
cat > "$MS3" <<'EOF'
|
|
82
|
+
## **METHODS**
|
|
83
|
+
Pooled estimates were computed in Python with descriptive statistics only.
|
|
84
|
+
|
|
85
|
+
## **RESULTS**
|
|
86
|
+
Pooled value 0.50.
|
|
87
|
+
EOF
|
|
88
|
+
cat > "$PR3" <<'EOF'
|
|
89
|
+
# PROSPERO Record
|
|
90
|
+
|
|
91
|
+
Synthesis: Freeman-Tukey transformation followed by random-effects pooling
|
|
92
|
+
(DerSimonian-Laird estimator).
|
|
93
|
+
EOF
|
|
94
|
+
python3 "$SCRIPT" --manuscript "$MS3" --prospero "$PR3" --out "$TMP/case3.json" --quiet
|
|
95
|
+
assert_exit "case 3: PROSPERO Freeman-Tukey, methods absent" 1 $?
|
|
96
|
+
python3 - "$TMP/case3.json" <<'PY' || fail=$((fail + 1))
|
|
97
|
+
import json, sys
|
|
98
|
+
with open(sys.argv[1]) as fh: rep = json.load(fh)
|
|
99
|
+
methods_listed = [s["method"] for s in rep["synthesis_method_drift"]]
|
|
100
|
+
assert "Freeman-Tukey" in methods_listed, methods_listed
|
|
101
|
+
PY
|
|
102
|
+
|
|
103
|
+
# --------------------------------------------------------------------------
|
|
104
|
+
# Case 4: no prospero supplied + clean manuscript = PASS.
|
|
105
|
+
# --------------------------------------------------------------------------
|
|
106
|
+
MS4="$TMP/case4.md"
|
|
107
|
+
cat > "$MS4" <<'EOF'
|
|
108
|
+
## **METHODS**
|
|
109
|
+
AUC = 0.700 on the validation set.
|
|
110
|
+
|
|
111
|
+
## **RESULTS**
|
|
112
|
+
External AUC = 0.700 (95% CI 0.65 to 0.75).
|
|
113
|
+
|
|
114
|
+
## **DISCUSSION**
|
|
115
|
+
The external AUC of 0.700 demonstrates ...
|
|
116
|
+
EOF
|
|
117
|
+
python3 "$SCRIPT" --manuscript "$MS4" --out "$TMP/case4.json" --quiet
|
|
118
|
+
assert_exit "case 4: clean, no prospero" 0 $?
|
|
119
|
+
|
|
120
|
+
echo ""
|
|
121
|
+
echo "ran=$ran fail=$fail"
|
|
122
|
+
[[ $fail -eq 0 ]]
|
|
@@ -0,0 +1,51 @@
|
|
|
1
|
+
#!/usr/bin/env bash
|
|
2
|
+
# Regression tests for verify_package_integrity.py --assert-vN-docx-changed.
|
|
3
|
+
|
|
4
|
+
set -uo pipefail
|
|
5
|
+
|
|
6
|
+
REPO_ROOT="$(cd "$(dirname "$0")/../../.." && pwd)"
|
|
7
|
+
SCRIPT="$REPO_ROOT/scripts/verify_package_integrity.py"
|
|
8
|
+
TMP="$(mktemp -d -t vNdocx.XXXXXX)"
|
|
9
|
+
trap 'rm -rf "$TMP"' EXIT
|
|
10
|
+
|
|
11
|
+
[[ -f "$SCRIPT" ]] || { echo "ENV-ERR: script missing" >&2; exit 2; }
|
|
12
|
+
|
|
13
|
+
fail=0
|
|
14
|
+
ran=0
|
|
15
|
+
assert_exit() {
|
|
16
|
+
local label="$1" expected="$2" actual="$3"
|
|
17
|
+
ran=$((ran + 1))
|
|
18
|
+
if [[ "$expected" == "$actual" ]]; then
|
|
19
|
+
printf ' PASS %-50s exit=%s\n' "$label" "$actual"
|
|
20
|
+
else
|
|
21
|
+
printf ' FAIL %-50s expected=%s actual=%s\n' "$label" "$expected" "$actual"
|
|
22
|
+
fail=$((fail + 1))
|
|
23
|
+
fi
|
|
24
|
+
}
|
|
25
|
+
|
|
26
|
+
# Case 1: identical bytes => FAIL
|
|
27
|
+
printf 'identical bytes\n' > "$TMP/vN.docx"
|
|
28
|
+
cp "$TMP/vN.docx" "$TMP/vNplus1.docx"
|
|
29
|
+
python3 "$SCRIPT" --assert-vN-docx-changed \
|
|
30
|
+
--vN-docx "$TMP/vN.docx" --new-docx "$TMP/vNplus1.docx" >/dev/null 2>&1
|
|
31
|
+
assert_exit "case 1: identical bytes (FAIL)" 1 $?
|
|
32
|
+
|
|
33
|
+
# Case 2: different bytes => PASS
|
|
34
|
+
printf 'different bytes for v_(N+1)\n' > "$TMP/vNplus1.docx"
|
|
35
|
+
python3 "$SCRIPT" --assert-vN-docx-changed \
|
|
36
|
+
--vN-docx "$TMP/vN.docx" --new-docx "$TMP/vNplus1.docx" >/dev/null 2>&1
|
|
37
|
+
assert_exit "case 2: different bytes (PASS)" 0 $?
|
|
38
|
+
|
|
39
|
+
# Case 3: missing v_N => exit 2
|
|
40
|
+
python3 "$SCRIPT" --assert-vN-docx-changed \
|
|
41
|
+
--vN-docx "$TMP/nonexistent.docx" --new-docx "$TMP/vNplus1.docx" >/dev/null 2>&1
|
|
42
|
+
assert_exit "case 3: missing v_N (exit 2)" 2 $?
|
|
43
|
+
|
|
44
|
+
# Case 4: missing --new-docx arg => exit 2
|
|
45
|
+
python3 "$SCRIPT" --assert-vN-docx-changed \
|
|
46
|
+
--vN-docx "$TMP/vN.docx" >/dev/null 2>&1
|
|
47
|
+
assert_exit "case 4: missing --new-docx (exit 2)" 2 $?
|
|
48
|
+
|
|
49
|
+
echo ""
|
|
50
|
+
echo "ran=$ran fail=$fail"
|
|
51
|
+
[[ $fail -eq 0 ]]
|