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.
Files changed (702) hide show
  1. package/LICENSE +50 -0
  2. package/README.md +602 -0
  3. package/README_FIRST.md +27 -0
  4. package/bin/medsci-skills.js +159 -0
  5. package/installers/install-macos.command +19 -0
  6. package/installers/install-windows.cmd +26 -0
  7. package/installers/install-windows.ps1 +17 -0
  8. package/installers/install.py +218 -0
  9. package/metadata/skills_catalog.json +452 -0
  10. package/package.json +48 -0
  11. package/skills/academic-aio/SKILL.md +408 -0
  12. package/skills/academic-aio/references/case_studies/kjr_mllm_2025.md +82 -0
  13. package/skills/academic-aio/references/checklists/AIO_GENERAL.md +354 -0
  14. package/skills/academic-aio/references/journal_summarybox_templates.yaml +126 -0
  15. package/skills/academic-aio/references/oac_funding_checklist.yaml +129 -0
  16. package/skills/academic-aio/references/reporting_guideline_mapping.md +39 -0
  17. package/skills/academic-aio/references/schema_markup_templates/CodeRepository.jsonld +32 -0
  18. package/skills/academic-aio/references/schema_markup_templates/Dataset.jsonld +36 -0
  19. package/skills/academic-aio/references/schema_markup_templates/Person.jsonld +30 -0
  20. package/skills/academic-aio/references/schema_markup_templates/README.md +43 -0
  21. package/skills/academic-aio/references/schema_markup_templates/ScholarlyArticle.jsonld +55 -0
  22. package/skills/academic-aio/scripts/batch_metadata_audit.py +169 -0
  23. package/skills/academic-aio/scripts/validate_schema.py +118 -0
  24. package/skills/academic-aio/skill.yml +36 -0
  25. package/skills/academic-aio/templates/aio_audit_checklist.md.j2 +108 -0
  26. package/skills/add-journal/SKILL.md +482 -0
  27. package/skills/add-journal/skill.yml +33 -0
  28. package/skills/analyze-stats/SKILL.md +598 -0
  29. package/skills/analyze-stats/references/analysis_guides/missing_data.md +109 -0
  30. package/skills/analyze-stats/references/analysis_guides/nhis_icd10_mapping.md +247 -0
  31. package/skills/analyze-stats/references/analysis_guides/propensity_score.md +132 -0
  32. package/skills/analyze-stats/references/analysis_guides/regression.md +115 -0
  33. package/skills/analyze-stats/references/analysis_guides/repeated_measures.md +160 -0
  34. package/skills/analyze-stats/references/analysis_guides/survey_weighted.md +366 -0
  35. package/skills/analyze-stats/references/analysis_guides/test_selection.md +86 -0
  36. package/skills/analyze-stats/references/style/figure_style.mplstyle +69 -0
  37. package/skills/analyze-stats/references/style/theme_publication.R +147 -0
  38. package/skills/analyze-stats/references/table-standards/journal-profiles/ajr.yaml +51 -0
  39. package/skills/analyze-stats/references/table-standards/journal-profiles/european_radiology.yaml +55 -0
  40. package/skills/analyze-stats/references/table-standards/journal-profiles/jama.yaml +66 -0
  41. package/skills/analyze-stats/references/table-standards/journal-profiles/lancet.yaml +57 -0
  42. package/skills/analyze-stats/references/table-standards/journal-profiles/nejm.yaml +51 -0
  43. package/skills/analyze-stats/references/table-standards/journal-profiles/radiology.yaml +66 -0
  44. package/skills/analyze-stats/references/table-standards/table-standards.md +287 -0
  45. package/skills/analyze-stats/references/table-standards/table-types/diagnostic_accuracy.md +36 -0
  46. package/skills/analyze-stats/references/table-standards/table-types/meta_analysis.md +58 -0
  47. package/skills/analyze-stats/references/table-standards/table-types/model_comparison.md +36 -0
  48. package/skills/analyze-stats/references/table-standards/table-types/regression_results.md +50 -0
  49. package/skills/analyze-stats/references/table-standards/table-types/table1_demographics.md +51 -0
  50. package/skills/analyze-stats/references/table-standards/tool-comparison.md +79 -0
  51. package/skills/analyze-stats/references/templates/agreement_analysis.py +436 -0
  52. package/skills/analyze-stats/references/templates/dca_plot.R +237 -0
  53. package/skills/analyze-stats/references/templates/diagnostic_accuracy.py +401 -0
  54. package/skills/analyze-stats/references/templates/dta_meta_analysis.R +384 -0
  55. package/skills/analyze-stats/references/templates/forest_plot.py +412 -0
  56. package/skills/analyze-stats/references/templates/likert_summary.py +356 -0
  57. package/skills/analyze-stats/references/templates/meta_analysis.R +365 -0
  58. package/skills/analyze-stats/references/templates/propensity_score.py +478 -0
  59. package/skills/analyze-stats/references/templates/regression.py +425 -0
  60. package/skills/analyze-stats/references/templates/repeated_measures.py +434 -0
  61. package/skills/analyze-stats/references/templates/sample_size.R +382 -0
  62. package/skills/analyze-stats/references/templates/survey_weighted_analysis.py +411 -0
  63. package/skills/analyze-stats/references/templates/survival_analysis.py +325 -0
  64. package/skills/analyze-stats/references/templates/table1_demographics.py +287 -0
  65. package/skills/analyze-stats/scripts/check_generated_code.py +335 -0
  66. package/skills/analyze-stats/skill.yml +38 -0
  67. package/skills/analyze-stats/tests/fixtures/gen_bad.R +16 -0
  68. package/skills/analyze-stats/tests/fixtures/gen_bad.py +24 -0
  69. package/skills/analyze-stats/tests/fixtures/gen_clean.py +21 -0
  70. package/skills/analyze-stats/tests/test_generated_code.sh +59 -0
  71. package/skills/analyze-stats/tests/test_survival_template.sh +53 -0
  72. package/skills/author-strategy/SKILL.md +117 -0
  73. package/skills/author-strategy/analyze_patterns.py +303 -0
  74. package/skills/author-strategy/fetch_pubmed.py +374 -0
  75. package/skills/author-strategy/skill.yml +34 -0
  76. package/skills/batch-cohort/SKILL.md +223 -0
  77. package/skills/batch-cohort/references/base_template_knhanes.R +210 -0
  78. package/skills/batch-cohort/references/batch_template_generator.R +222 -0
  79. package/skills/batch-cohort/references/variable_coding_registry.md +136 -0
  80. package/skills/batch-cohort/skill.yml +35 -0
  81. package/skills/calc-sample-size/SKILL.md +491 -0
  82. package/skills/calc-sample-size/references/formulas.md +655 -0
  83. package/skills/calc-sample-size/references/observational_cohort.md +49 -0
  84. package/skills/calc-sample-size/skill.yml +51 -0
  85. package/skills/check-reporting/SKILL.md +534 -0
  86. package/skills/check-reporting/references/LICENSES.md +41 -0
  87. package/skills/check-reporting/references/checklists/AMSTAR2.md +54 -0
  88. package/skills/check-reporting/references/checklists/ARRIVE_2.md +234 -0
  89. package/skills/check-reporting/references/checklists/CARE.md +102 -0
  90. package/skills/check-reporting/references/checklists/CLAIM_2024.md +128 -0
  91. package/skills/check-reporting/references/checklists/CLEAR.md +113 -0
  92. package/skills/check-reporting/references/checklists/CONSORT.md +86 -0
  93. package/skills/check-reporting/references/checklists/COSMIN_RoB.md +136 -0
  94. package/skills/check-reporting/references/checklists/GRRAS.md +61 -0
  95. package/skills/check-reporting/references/checklists/MI_CLEAR_LLM.md +167 -0
  96. package/skills/check-reporting/references/checklists/MOOSE.md +85 -0
  97. package/skills/check-reporting/references/checklists/NOS.md +88 -0
  98. package/skills/check-reporting/references/checklists/PRISMA_2020.md +135 -0
  99. package/skills/check-reporting/references/checklists/PRISMA_DTA.md +36 -0
  100. package/skills/check-reporting/references/checklists/PRISMA_P.md +56 -0
  101. package/skills/check-reporting/references/checklists/PROBAST.md +75 -0
  102. package/skills/check-reporting/references/checklists/PROBAST_AI.md +130 -0
  103. package/skills/check-reporting/references/checklists/QUADAS2.md +77 -0
  104. package/skills/check-reporting/references/checklists/QUADAS_C.md +131 -0
  105. package/skills/check-reporting/references/checklists/ROBINS_E.md +179 -0
  106. package/skills/check-reporting/references/checklists/ROBINS_I.md +87 -0
  107. package/skills/check-reporting/references/checklists/ROBIS.md +114 -0
  108. package/skills/check-reporting/references/checklists/ROB_ME.md +126 -0
  109. package/skills/check-reporting/references/checklists/RoB2.md +79 -0
  110. package/skills/check-reporting/references/checklists/RoB_NMA.md +96 -0
  111. package/skills/check-reporting/references/checklists/SPIRIT.md +112 -0
  112. package/skills/check-reporting/references/checklists/SQUIRE_2.md +68 -0
  113. package/skills/check-reporting/references/checklists/STARD.md +129 -0
  114. package/skills/check-reporting/references/checklists/STARD_AI.md +211 -0
  115. package/skills/check-reporting/references/checklists/STROBE.md +80 -0
  116. package/skills/check-reporting/references/checklists/SWiM.md +33 -0
  117. package/skills/check-reporting/references/checklists/TRIPOD.md +157 -0
  118. package/skills/check-reporting/references/checklists/TRIPOD_AI.md +140 -0
  119. package/skills/check-reporting/references/step4c_registration_timing.md +93 -0
  120. package/skills/check-reporting/references/step4d_prisma_figure_audit.md +137 -0
  121. package/skills/check-reporting/scripts/check_checklist_exists.py +183 -0
  122. package/skills/check-reporting/scripts/check_checklist_version.py +168 -0
  123. package/skills/check-reporting/scripts/check_framework_naming.py +206 -0
  124. package/skills/check-reporting/scripts/check_prisma_figure.py +209 -0
  125. package/skills/check-reporting/scripts/prisma_cascade_check.py +274 -0
  126. package/skills/check-reporting/skill.yml +41 -0
  127. package/skills/check-reporting/tests/fixtures/framework_bad.md +8 -0
  128. package/skills/check-reporting/tests/fixtures/framework_clean.md +7 -0
  129. package/skills/check-reporting/tests/test_checklist_fail_fast.sh +77 -0
  130. package/skills/check-reporting/tests/test_checklist_version.sh +72 -0
  131. package/skills/check-reporting/tests/test_framework_naming.sh +45 -0
  132. package/skills/check-reporting/tests/test_prisma_cascade.sh +104 -0
  133. package/skills/clean-data/SKILL.md +180 -0
  134. package/skills/clean-data/references/cleaning_patterns.md +299 -0
  135. package/skills/clean-data/references/profiling_template.py +304 -0
  136. package/skills/clean-data/scripts/check_structural_zero.py +174 -0
  137. package/skills/clean-data/skill.yml +35 -0
  138. package/skills/clean-data/tests/fixtures/smoking.csv +8 -0
  139. package/skills/clean-data/tests/test_structural_zero.sh +49 -0
  140. package/skills/cross-national/SKILL.md +264 -0
  141. package/skills/cross-national/skill.yml +37 -0
  142. package/skills/define-variables/SKILL.md +146 -0
  143. package/skills/define-variables/references/common_definitions.md +190 -0
  144. package/skills/define-variables/skill.yml +34 -0
  145. package/skills/define-variables/templates/variable_operationalization.md +64 -0
  146. package/skills/deidentify/SKILL.md +203 -0
  147. package/skills/deidentify/deidentify.py +1224 -0
  148. package/skills/deidentify/locales/_template.json +45 -0
  149. package/skills/deidentify/locales/au.json +43 -0
  150. package/skills/deidentify/locales/ca.json +44 -0
  151. package/skills/deidentify/locales/cn.json +47 -0
  152. package/skills/deidentify/locales/de.json +48 -0
  153. package/skills/deidentify/locales/fr.json +48 -0
  154. package/skills/deidentify/locales/in.json +48 -0
  155. package/skills/deidentify/locales/jp.json +48 -0
  156. package/skills/deidentify/locales/kr.json +48 -0
  157. package/skills/deidentify/locales/uk.json +45 -0
  158. package/skills/deidentify/locales/us.json +43 -0
  159. package/skills/deidentify/references/date_shift_guide.md +82 -0
  160. package/skills/deidentify/references/hipaa_18_identifiers.md +48 -0
  161. package/skills/deidentify/references/korean_phi_patterns.md +135 -0
  162. package/skills/deidentify/skill.yml +43 -0
  163. package/skills/deidentify/tests/README.md +26 -0
  164. package/skills/deidentify/tests/test_clean.csv +16 -0
  165. package/skills/deidentify/tests/test_edge_cases.csv +11 -0
  166. package/skills/deidentify/tests/test_phi_korean.csv +11 -0
  167. package/skills/design-ai-benchmarking/SKILL.md +214 -0
  168. package/skills/design-ai-benchmarking/references/benchmark_export_schema.json +69 -0
  169. package/skills/design-ai-benchmarking/references/elicitation_rubric_template.md +37 -0
  170. package/skills/design-ai-benchmarking/skill.yml +38 -0
  171. package/skills/design-study/SKILL.md +298 -0
  172. package/skills/design-study/skill.yml +33 -0
  173. package/skills/fill-icmje-coi/SKILL.md +216 -0
  174. package/skills/fill-icmje-coi/scripts/fill_icmje_coi.py +140 -0
  175. package/skills/fill-icmje-coi/skill.yml +35 -0
  176. package/skills/fill-icmje-coi/templates/icmje_coi_seed_synthetic.docx +0 -0
  177. package/skills/fill-protocol/SKILL.md +248 -0
  178. package/skills/fill-protocol/examples/example_irb_template.yaml +53 -0
  179. package/skills/fill-protocol/references/best_practices.md +121 -0
  180. package/skills/fill-protocol/scripts/doc_to_docx.py +111 -0
  181. package/skills/fill-protocol/scripts/fill_form.py +611 -0
  182. package/skills/fill-protocol/scripts/inspect_template.py +61 -0
  183. package/skills/fill-protocol/setup.sh +162 -0
  184. package/skills/fill-protocol/skill.yml +37 -0
  185. package/skills/find-cohort-gap/SKILL.md +309 -0
  186. package/skills/find-cohort-gap/references/cohort_profile_template.md +93 -0
  187. package/skills/find-cohort-gap/references/onepager_template.md +84 -0
  188. package/skills/find-cohort-gap/references/pattern_scoring_rubric.md +169 -0
  189. package/skills/find-cohort-gap/references/saturation_query_templates.md +143 -0
  190. package/skills/find-cohort-gap/skill.yml +35 -0
  191. package/skills/find-journal/POLICY.md +87 -0
  192. package/skills/find-journal/SKILL.md +340 -0
  193. package/skills/find-journal/references/journal_profiles/AJNR.md +29 -0
  194. package/skills/find-journal/references/journal_profiles/AJR.md +30 -0
  195. package/skills/find-journal/references/journal_profiles/Abdominal_Radiology.md +30 -0
  196. package/skills/find-journal/references/journal_profiles/Academic_Radiology.md +30 -0
  197. package/skills/find-journal/references/journal_profiles/Annals_of_Internal_Medicine.md +33 -0
  198. package/skills/find-journal/references/journal_profiles/Artificial_Intelligence_in_Medicine.md +28 -0
  199. package/skills/find-journal/references/journal_profiles/BMC_Medicine.md +31 -0
  200. package/skills/find-journal/references/journal_profiles/British_Journal_of_Radiology.md +39 -0
  201. package/skills/find-journal/references/journal_profiles/CVIR.md +30 -0
  202. package/skills/find-journal/references/journal_profiles/Chest.md +39 -0
  203. package/skills/find-journal/references/journal_profiles/Clinical_Radiology.md +30 -0
  204. package/skills/find-journal/references/journal_profiles/Clinical_and_Molecular_Hepatology.md +32 -0
  205. package/skills/find-journal/references/journal_profiles/Diabetes_Metabolism_Journal.md +36 -0
  206. package/skills/find-journal/references/journal_profiles/Diagnostic_and_Interventional_Radiology.md +32 -0
  207. package/skills/find-journal/references/journal_profiles/Endocrinology_and_Metabolism.md +37 -0
  208. package/skills/find-journal/references/journal_profiles/European_Journal_of_Preventive_Cardiology.md +39 -0
  209. package/skills/find-journal/references/journal_profiles/European_Radiology.md +29 -0
  210. package/skills/find-journal/references/journal_profiles/Hepatology_Communications.md +40 -0
  211. package/skills/find-journal/references/journal_profiles/Hepatology_International.md +37 -0
  212. package/skills/find-journal/references/journal_profiles/IEEE_JBHI.md +28 -0
  213. package/skills/find-journal/references/journal_profiles/IEEE_TMI.md +28 -0
  214. package/skills/find-journal/references/journal_profiles/INSI.md +29 -0
  215. package/skills/find-journal/references/journal_profiles/Investigative_Radiology.md +25 -0
  216. package/skills/find-journal/references/journal_profiles/JACC_Advances.md +41 -0
  217. package/skills/find-journal/references/journal_profiles/JACC_Asia.md +30 -0
  218. package/skills/find-journal/references/journal_profiles/JACR.md +28 -0
  219. package/skills/find-journal/references/journal_profiles/JAMA.md +40 -0
  220. package/skills/find-journal/references/journal_profiles/JAMA_Network_Open.md +30 -0
  221. package/skills/find-journal/references/journal_profiles/JCSM.md +39 -0
  222. package/skills/find-journal/references/journal_profiles/JKMS.md +32 -0
  223. package/skills/find-journal/references/journal_profiles/JMIR.md +29 -0
  224. package/skills/find-journal/references/journal_profiles/JMIR_Medical_Education.md +29 -0
  225. package/skills/find-journal/references/journal_profiles/JNIS.md +35 -0
  226. package/skills/find-journal/references/journal_profiles/JVIR.md +31 -0
  227. package/skills/find-journal/references/journal_profiles/Journal_of_Biomedical_Informatics.md +29 -0
  228. package/skills/find-journal/references/journal_profiles/Journal_of_Clinical_Endocrinology_and_Metabolism.md +40 -0
  229. package/skills/find-journal/references/journal_profiles/Journal_of_Magnetic_Resonance_Imaging.md +30 -0
  230. package/skills/find-journal/references/journal_profiles/Journal_of_Nuclear_Medicine.md +31 -0
  231. package/skills/find-journal/references/journal_profiles/Journal_of_Stroke.md +32 -0
  232. package/skills/find-journal/references/journal_profiles/KJR.md +38 -0
  233. package/skills/find-journal/references/journal_profiles/Korean_Circulation_Journal.md +38 -0
  234. package/skills/find-journal/references/journal_profiles/Korean_Journal_of_Internal_Medicine.md +36 -0
  235. package/skills/find-journal/references/journal_profiles/Lancet_Diabetes_and_Endocrinology.md +40 -0
  236. package/skills/find-journal/references/journal_profiles/Lancet_Gastroenterology_and_Hepatology.md +49 -0
  237. package/skills/find-journal/references/journal_profiles/Lancet_Infectious_Diseases.md +38 -0
  238. package/skills/find-journal/references/journal_profiles/Lancet_Neurology.md +39 -0
  239. package/skills/find-journal/references/journal_profiles/Lancet_Oncology.md +40 -0
  240. package/skills/find-journal/references/journal_profiles/Lancet_Psychiatry.md +38 -0
  241. package/skills/find-journal/references/journal_profiles/Lancet_Public_Health.md +30 -0
  242. package/skills/find-journal/references/journal_profiles/Lancet_Respiratory_Medicine.md +39 -0
  243. package/skills/find-journal/references/journal_profiles/Liver_International.md +33 -0
  244. package/skills/find-journal/references/journal_profiles/Medical_Image_Analysis.md +28 -0
  245. package/skills/find-journal/references/journal_profiles/NEJM.md +33 -0
  246. package/skills/find-journal/references/journal_profiles/Nature_Machine_Intelligence.md +31 -0
  247. package/skills/find-journal/references/journal_profiles/Nature_Medicine.md +39 -0
  248. package/skills/find-journal/references/journal_profiles/Neuroradiology.md +31 -0
  249. package/skills/find-journal/references/journal_profiles/Nutrition_Metabolism_and_Cardiovascular_Diseases.md +39 -0
  250. package/skills/find-journal/references/journal_profiles/PLOS_Medicine.md +32 -0
  251. package/skills/find-journal/references/journal_profiles/RYAI.md +28 -0
  252. package/skills/find-journal/references/journal_profiles/Radiology.md +29 -0
  253. package/skills/find-journal/references/journal_profiles/Skeletal_Radiology.md +31 -0
  254. package/skills/find-journal/references/journal_profiles/Stroke.md +37 -0
  255. package/skills/find-journal/references/journal_profiles/The_BMJ.md +31 -0
  256. package/skills/find-journal/references/journal_profiles/The_Lancet.md +31 -0
  257. package/skills/find-journal/references/journal_profiles/The_Lancet_Digital_Health.md +29 -0
  258. package/skills/find-journal/references/journal_profiles/World_Journal_of_Hepatology.md +53 -0
  259. package/skills/find-journal/references/journal_profiles/npj_Digital_Medicine.md +29 -0
  260. package/skills/find-journal/skill.yml +34 -0
  261. package/skills/fulltext-retrieval/SKILL.md +174 -0
  262. package/skills/fulltext-retrieval/fetch_oa.py +433 -0
  263. package/skills/fulltext-retrieval/pdf_to_md.py +160 -0
  264. package/skills/fulltext-retrieval/skill.yml +41 -0
  265. package/skills/generate-codebook/SKILL.md +155 -0
  266. package/skills/generate-codebook/references/codebook_schema.md +76 -0
  267. package/skills/generate-codebook/scripts/generate_codebook.py +278 -0
  268. package/skills/generate-codebook/skill.yml +35 -0
  269. package/skills/generate-codebook/tests/test_generate_codebook.sh +76 -0
  270. package/skills/grant-builder/SKILL.md +251 -0
  271. package/skills/grant-builder/skill.yml +34 -0
  272. package/skills/humanize/SKILL.md +251 -0
  273. package/skills/humanize/references/ai_patterns.md +571 -0
  274. package/skills/humanize/skill.yml +33 -0
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@@ -0,0 +1,44 @@
1
+ #!/usr/bin/env bash
2
+ # Regression test for the multi-copy manuscript divergence detector (Phase 8).
3
+ # Synthetic fixtures: an SSOT and two copies — one reworded but claim-complete
4
+ # (OK), one missing an SSOT claim (p = 0.074, an unpropagated edit). Stdlib-only.
5
+ set -u
6
+
7
+ HERE="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
8
+ SCRIPT="$HERE/../scripts/detect_copy_divergence.py"
9
+ SSOT="$HERE/fixtures/ssot.md"
10
+ OKC="$HERE/fixtures/copy_ok.md"
11
+ STALE="$HERE/fixtures/copy_stale.md"
12
+ OUT="$(mktemp -t cd_XXXX).json"
13
+ trap 'rm -f "$OUT"' EXIT
14
+
15
+ fail=0
16
+ check() { local label="$1"; shift
17
+ if "$@" >/dev/null 2>&1; then printf ' PASS %s\n' "$label"
18
+ else printf ' FAIL %s\n' "$label"; fail=$((fail+1)); fi
19
+ }
20
+
21
+ [[ -f "$SCRIPT" ]] || { echo "ENV-ERR: script missing" >&2; exit 2; }
22
+
23
+ # OK copy alone -> exit 0.
24
+ python3 "$SCRIPT" --ssot "$SSOT" --copy "$OKC" --strict >/dev/null 2>&1
25
+ check "exit 0 when the copy carries every SSOT claim" test "$?" -eq 0
26
+
27
+ # Stale copy -> exit 1, flags the unpropagated claim.
28
+ python3 "$SCRIPT" --ssot "$SSOT" --copy "$OKC" --copy "$STALE" --out "$OUT" --strict >/dev/null 2>&1
29
+ check "exit 1 when a copy is missing an SSOT claim" test "$?" -eq 1
30
+ check "verdict DIVERGENT" python3 -c "
31
+ import json; assert json.load(open('$OUT'))['verdict']=='DIVERGENT'"
32
+ check "stale copy flags the unpropagated p-value" python3 -c "
33
+ import json
34
+ d=json.load(open('$OUT'))
35
+ stale=[c for c in d['copies'] if c['verdict']=='STALE_COPY']
36
+ assert stale and any('p=0.074' in u for u in stale[0]['unpropagated_to_copy'])"
37
+ check "OK copy not flagged" python3 -c "
38
+ import json
39
+ d=json.load(open('$OUT'))
40
+ ok=[c for c in d['copies'] if c['copy'].endswith('copy_ok.md')]
41
+ assert ok and ok[0]['verdict']=='OK'"
42
+
43
+ echo "fail=$fail"; [[ "$fail" -eq 0 ]] && echo "ALL PASS" || echo "FAILURES: $fail"
44
+ exit "$fail"
@@ -0,0 +1,80 @@
1
+ #!/usr/bin/env bash
2
+ # Test scripts/check_cross_artifact_stale.py — the A3 cross-artifact staleness gate.
3
+ # Synthetic, PII-free fixtures: a body that corrects two labeled values, a stale
4
+ # supplement that disagrees, a checklist built against an older manuscript version,
5
+ # and a clean supplement that agrees.
6
+ set -u
7
+
8
+ HERE="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
9
+ SCRIPT="$HERE/../scripts/check_cross_artifact_stale.py"
10
+ PASS=0
11
+ FAIL=0
12
+ ok() { echo " PASS: $1"; PASS=$((PASS+1)); }
13
+ bad() { echo " FAIL: $1"; FAIL=$((FAIL+1)); }
14
+
15
+ WORK="$(mktemp -d)"
16
+ trap 'rm -rf "$WORK"' EXIT
17
+
18
+ # body (v8 in filename) — corrected values
19
+ cat > "$WORK/manuscript_v8.md" <<'EOF'
20
+ ## Results
21
+ The complete-case analysis included 95.7% of the cohort.
22
+ Inter-rater agreement was substantial (kappa = 0.923).
23
+ EOF
24
+
25
+ # stale supplement: disagreeing values for the same labels
26
+ mkdir -p "$WORK/aux"
27
+ cat > "$WORK/aux/supplement.md" <<'EOF'
28
+ Footnote: complete-case retention was 7.5% after exclusions.
29
+ Reliability sub-analysis: kappa = 0.904.
30
+ EOF
31
+
32
+ # checklist built against an older manuscript version
33
+ cat > "$WORK/aux/strobe_checklist.md" <<'EOF'
34
+ Target manuscript: cohort study v6 (2026-04-20)
35
+ Item 13: see Results, line 42.
36
+ EOF
37
+
38
+ # clean supplement that agrees with the body
39
+ mkdir -p "$WORK/clean"
40
+ cat > "$WORK/clean/supplement.md" <<'EOF'
41
+ Footnote: complete-case retention was 95.7%.
42
+ Reliability: kappa = 0.923.
43
+ EOF
44
+
45
+ run() { python3 "$SCRIPT" "$@" 2>/dev/null; }
46
+
47
+ # 1. drift + version-stale -> exit 1
48
+ run --manuscript "$WORK/manuscript_v8.md" --aux "$WORK/aux" --quiet
49
+ [ $? -eq 1 ] && ok "stale aux + old checklist version -> exit 1" || bad "should fail"
50
+
51
+ # 2. JSON reports both finding types
52
+ run --manuscript "$WORK/manuscript_v8.md" --aux "$WORK/aux" --out "$WORK/r.json" --quiet
53
+ python3 -c "
54
+ import json,sys
55
+ d=json.load(open('$WORK/r.json'))
56
+ types={f['type'] for f in d['findings']}
57
+ sys.exit(0 if {'labeled_value_drift','checklist_version_stale'} <= types
58
+ and d['summary']['stale'] >= 2 and d['summary']['version_stale'] >= 1 else 1)
59
+ " && ok "JSON: labeled_value_drift (kappa+complete_case) + version_stale" || bad "JSON findings incomplete"
60
+
61
+ # 3. explicit --manuscript-version overrides filename inference
62
+ run --manuscript "$WORK/manuscript_v8.md" --aux "$WORK/aux/strobe_checklist.md" \
63
+ --manuscript-version v8 --out "$WORK/r2.json" --quiet
64
+ python3 -c "
65
+ import json,sys
66
+ d=json.load(open('$WORK/r2.json'))
67
+ sys.exit(0 if d['summary']['version_stale'] == 1 else 1)
68
+ " && ok "explicit --manuscript-version flags stale checklist" || bad "version flag failed"
69
+
70
+ # 4. clean supplement that agrees -> exit 0
71
+ run --manuscript "$WORK/manuscript_v8.md" --aux "$WORK/clean" --quiet
72
+ [ $? -eq 0 ] && ok "agreeing supplement passes" || bad "agreeing supplement should pass"
73
+
74
+ # 5. missing --aux -> usage error (exit 2)
75
+ run --manuscript "$WORK/manuscript_v8.md" --quiet
76
+ [ $? -eq 2 ] && ok "missing --aux -> exit 2" || bad "missing --aux should be usage error"
77
+
78
+ echo ""
79
+ echo "test_cross_artifact_stale: $PASS passed, $FAIL failed"
80
+ [ "$FAIL" -eq 0 ]
@@ -0,0 +1,132 @@
1
+ #!/usr/bin/env bash
2
+ # Regression tests for sync-submission cross_document_n_check.py.
3
+ #
4
+ # Synthetic fixtures only (no project paths, no manuscript IDs).
5
+ # Skip with NETWORK=0 — this script does not use the network.
6
+ #
7
+ # Usage:
8
+ # skills/sync-submission/tests/test_cross_document_n.sh
9
+ # Exit codes:
10
+ # 0 — all tests passed
11
+ # 1 — at least one test regressed
12
+ # 2 — environment problem
13
+
14
+ set -uo pipefail
15
+
16
+ REPO_ROOT="$(cd "$(dirname "$0")/../../.." && pwd)"
17
+ SCRIPT="$REPO_ROOT/skills/sync-submission/scripts/cross_document_n_check.py"
18
+ TMP="$(mktemp -d -t cross_doc_n.XXXXXX)"
19
+ trap 'rm -rf "$TMP"' EXIT
20
+
21
+ if [[ ! -f "$SCRIPT" ]]; then
22
+ echo "ENV-ERR: script not found at $SCRIPT" >&2
23
+ exit 2
24
+ fi
25
+ command -v python3 >/dev/null 2>&1 || { echo "ENV-ERR: python3 missing" >&2; exit 2; }
26
+
27
+ fail=0
28
+ ran=0
29
+
30
+ assert_exit() {
31
+ local label="$1" expected="$2" actual="$3"
32
+ ran=$((ran + 1))
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 ]]