medsci-skills 5.26.2 → 5.28.0

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 (91) hide show
  1. package/THIRD-PARTY-NOTICES.md +1 -1
  2. package/metadata/distribution_files.json +280 -85
  3. package/metadata/distribution_manifest.json +1 -1
  4. package/package.json +1 -1
  5. package/skills/analyze-stats/SKILL.md +20 -23
  6. package/skills/analyze-stats/references/analysis_run_workflow.md +150 -0
  7. package/skills/analyze-stats/references/table-standards/table-types/incremental_value.md +71 -27
  8. package/skills/analyze-stats/references/templates/diagnostic_accuracy.py +16 -21
  9. package/skills/analyze-stats/scripts/analysis_run_challenge/README.md +12 -0
  10. package/skills/analyze-stats/scripts/analysis_run_challenge/verify.sh +34 -0
  11. package/skills/analyze-stats/scripts/demo_analysis_run.py +43 -0
  12. package/skills/analyze-stats/scripts/run_analysis.py +322 -0
  13. package/skills/analyze-stats/skill.yml +5 -1
  14. package/skills/analyze-stats/tests/test_analysis_run.py +325 -0
  15. package/skills/check-reporting/SKILL.md +0 -2
  16. package/skills/check-reporting/references/checklists/STARD_AI.md +36 -4
  17. package/skills/contribute/tests/test_contribution_safety.sh +14 -2
  18. package/skills/deidentify/deidentify.py +22 -12
  19. package/skills/deidentify/tests/test_deidentify_scan.sh +65 -0
  20. package/skills/design-study/SKILL.md +0 -2
  21. package/skills/fill-protocol/SKILL.md +0 -2
  22. package/skills/find-cohort-gap/SKILL.md +0 -2
  23. package/skills/find-journal/references/journal_profiles/Annals_of_Oncology.md +47 -0
  24. package/skills/find-journal/references/journal_profiles/BJR_Case_Reports.md +1 -1
  25. package/skills/find-journal/references/journal_profiles/BMJ_Case_Reports.md +1 -1
  26. package/skills/find-journal/references/journal_profiles/CVIR.md +1 -1
  27. package/skills/find-journal/references/journal_profiles/Cancer_Research_and_Treatment.md +47 -0
  28. package/skills/find-journal/references/journal_profiles/Chest.md +1 -1
  29. package/skills/find-journal/references/journal_profiles/Clinical_Cancer_Research.md +53 -0
  30. package/skills/find-journal/references/journal_profiles/Cureus.md +1 -1
  31. package/skills/find-journal/references/journal_profiles/ESMO_Open.md +49 -0
  32. package/skills/find-journal/references/journal_profiles/Journal_of_Breast_Cancer.md +51 -0
  33. package/skills/find-journal/references/journal_profiles/Journal_of_Clinical_Oncology.md +51 -0
  34. package/skills/find-journal/references/journal_profiles/Journal_of_Medical_Case_Reports.md +1 -1
  35. package/skills/find-journal/references/journal_profiles/Radiology_Case_Reports.md +1 -1
  36. package/skills/find-journal/references/journal_profiles/The_Lancet_Digital_Health.md +1 -1
  37. package/skills/find-journal/references/journal_profiles/npj_Breast_Cancer.md +50 -0
  38. package/skills/grant-builder/SKILL.md +0 -2
  39. package/skills/make-figures/SKILL.md +1 -2
  40. package/skills/make-figures/references/exemplar_plots/README.md +25 -0
  41. package/skills/make-figures/references/exemplar_plots/cumulative_incidence.md +46 -0
  42. package/skills/make-figures/references/exemplar_plots/shap_beeswarm.md +60 -0
  43. package/skills/make-figures/references/exemplar_plots/spider_plot.md +44 -0
  44. package/skills/make-figures/references/exemplar_plots/swimmer_plot.md +46 -0
  45. package/skills/make-figures/references/exemplar_plots/waterfall_plot.md +48 -0
  46. package/skills/manage-refs/citation_styles/README.md +20 -1
  47. package/skills/manage-refs/citation_styles/american-association-for-cancer-research.csl +245 -0
  48. package/skills/manage-refs/citation_styles/annals-of-oncology.csl +312 -0
  49. package/skills/manage-refs/citation_styles/breast-cancer-research-and-treatment.csl +19 -0
  50. package/skills/manage-refs/citation_styles/clinical-breast-cancer.csl +14 -0
  51. package/skills/manage-refs/citation_styles/clinical-cancer-research.csl +17 -0
  52. package/skills/manage-refs/citation_styles/elsevier-vancouver.csl +163 -0
  53. package/skills/manage-refs/citation_styles/journal-of-breast-cancer.csl +251 -0
  54. package/skills/manage-refs/citation_styles/journal-of-clinical-oncology.csl +139 -0
  55. package/skills/manage-refs/citation_styles/the-breast.csl +14 -0
  56. package/skills/manage-refs/citation_styles/the-lancet-oncology.csl +16 -0
  57. package/skills/manage-refs/citation_styles/the-lancet.csl +181 -0
  58. package/skills/present-paper/SKILL.md +0 -2
  59. package/skills/revise/SKILL.md +0 -2
  60. package/skills/self-review/SKILL.md +0 -2
  61. package/skills/sync-submission/SKILL.md +18 -2
  62. package/skills/sync-submission/examples/build_synthetic_bundle.py +68 -0
  63. package/skills/sync-submission/references/bundle_workflow.md +130 -0
  64. package/skills/sync-submission/scripts/preflight_gate.py +34 -5
  65. package/skills/sync-submission/scripts/sync_submission.py +372 -102
  66. package/skills/sync-submission/skill.yml +3 -0
  67. package/skills/sync-submission/tests/test_preflight_gate.sh +16 -0
  68. package/skills/sync-submission/tests/test_submission_bundle.py +324 -0
  69. package/skills/verify-refs/SKILL.md +29 -3
  70. package/skills/verify-refs/references/claim_evidence_workflow.md +99 -0
  71. package/skills/verify-refs/scripts/_claim_evidence.py +254 -0
  72. package/skills/verify-refs/scripts/check_claim_fidelity.py +99 -17
  73. package/skills/verify-refs/scripts/claim_fidelity_challenge/verify.sh +4 -9
  74. package/skills/verify-refs/skill.yml +3 -0
  75. package/skills/verify-refs/tests/test_claim_evidence.py +276 -0
  76. package/skills/write-paper/SKILL.md +0 -2
  77. package/skills/write-paper/references/journal_profiles/Annals_of_Oncology.md +141 -0
  78. package/skills/write-paper/references/journal_profiles/Cancer_Research_and_Treatment.md +138 -0
  79. package/skills/write-paper/references/journal_profiles/Chest.md +1 -1
  80. package/skills/write-paper/references/journal_profiles/Clinical_Cancer_Research.md +154 -0
  81. package/skills/write-paper/references/journal_profiles/ESMO_Open.md +135 -0
  82. package/skills/write-paper/references/journal_profiles/JNIS.md +1 -1
  83. package/skills/write-paper/references/journal_profiles/Journal_of_Breast_Cancer.md +141 -0
  84. package/skills/write-paper/references/journal_profiles/Journal_of_Clinical_Oncology.md +154 -0
  85. package/skills/write-paper/references/journal_profiles/Journal_of_Stroke.md +1 -1
  86. package/skills/write-paper/references/journal_profiles/Liver_International.md +1 -1
  87. package/skills/write-paper/references/journal_profiles/NEJM_AI.md +1 -1
  88. package/skills/write-paper/references/journal_profiles/Stroke.md +1 -1
  89. package/skills/write-paper/references/journal_profiles/The_Lancet_Digital_Health.md +1 -1
  90. package/skills/write-paper/references/journal_profiles/npj_Breast_Cancer.md +143 -0
  91. package/skills/write-protocol/SKILL.md +0 -2
package/THIRD-PARTY-NOTICES.md CHANGED
@@ -47,7 +47,7 @@ long time after the 2025 versions had replaced them.
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  ### Citation styles (`skills/manage-refs/citation_styles/*.csl`)
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- 15 CSL files from the Citation Style Language project: **CC BY-SA 3.0**, unmodified, each retaining
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+ 27 CSL files from the Citation Style Language project: **CC BY-SA 3.0**, unmodified, each retaining
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  its own `<rights>` element. See `skills/manage-refs/NOTICE.md`.
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  ### Not bundled — download these yourself