@pikaa-ai/pikaa 0.3.1 → 0.3.5

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 (1870) hide show
  1. package/dist/cli.js +1181 -600
  2. package/dist/index.js +525 -204
  3. package/package.json +5 -3
  4. package/skills/adaptyv/references/api-endpoints.md +0 -690
  5. package/skills/aeon/references/anomaly_detection.md +0 -154
  6. package/skills/aeon/references/classification.md +0 -144
  7. package/skills/aeon/references/clustering.md +0 -123
  8. package/skills/aeon/references/datasets_benchmarking.md +0 -392
  9. package/skills/aeon/references/distances.md +0 -256
  10. package/skills/aeon/references/forecasting.md +0 -109
  11. package/skills/aeon/references/networks.md +0 -289
  12. package/skills/aeon/references/regression.md +0 -118
  13. package/skills/aeon/references/segmentation.md +0 -163
  14. package/skills/aeon/references/similarity_search.md +0 -187
  15. package/skills/aeon/references/transformations.md +0 -246
  16. package/skills/analytical-method-validation/assets/validation-protocol-template.md +0 -106
  17. package/skills/analytical-method-validation/assets/validation-report-template.md +0 -116
  18. package/skills/analytical-method-validation/references/compendial-and-clsi.md +0 -96
  19. package/skills/analytical-method-validation/references/framework-selection.md +0 -87
  20. package/skills/analytical-method-validation/references/ich-m10-bioanalytical.md +0 -123
  21. package/skills/analytical-method-validation/references/ich-q2r2.md +0 -229
  22. package/skills/analytical-method-validation/references/source-ledger.md +0 -125
  23. package/skills/analytical-method-validation/references/statistics.md +0 -209
  24. package/skills/analytical-method-validation/scripts/_catalog.py +0 -499
  25. package/skills/analytical-method-validation/scripts/_common.py +0 -955
  26. package/skills/analytical-method-validation/scripts/check_accuracy_precision.py +0 -328
  27. package/skills/analytical-method-validation/scripts/check_bioanalytical_run.py +0 -293
  28. package/skills/analytical-method-validation/scripts/check_detection_limits.py +0 -310
  29. package/skills/analytical-method-validation/scripts/check_response.py +0 -243
  30. package/skills/analytical-method-validation/scripts/compare_methods.py +0 -215
  31. package/skills/analytical-method-validation/scripts/plan_validation.py +0 -381
  32. package/skills/anndata/references/best_practices.md +0 -532
  33. package/skills/anndata/references/concatenation.md +0 -399
  34. package/skills/anndata/references/data_structure.md +0 -314
  35. package/skills/anndata/references/io_operations.md +0 -466
  36. package/skills/anndata/references/manipulation.md +0 -516
  37. package/skills/arbor/references/arbor-upstream.md +0 -91
  38. package/skills/arbor/references/executor-brief.md +0 -68
  39. package/skills/arbor/references/htr-methodology.md +0 -177
  40. package/skills/arbor/references/report-template.md +0 -39
  41. package/skills/arbor/scripts/tree.py +0 -564
  42. package/skills/arboreto/references/algorithms.md +0 -152
  43. package/skills/arboreto/references/basic_inference.md +0 -181
  44. package/skills/arboreto/references/distributed_computing.md +0 -242
  45. package/skills/arboreto/scripts/basic_grn_inference.py +0 -107
  46. package/skills/astropy/references/coordinates.md +0 -280
  47. package/skills/astropy/references/cosmology.md +0 -309
  48. package/skills/astropy/references/fits.md +0 -398
  49. package/skills/astropy/references/tables.md +0 -495
  50. package/skills/astropy/references/time.md +0 -412
  51. package/skills/astropy/references/units.md +0 -178
  52. package/skills/astropy/references/wcs_and_other_modules.md +0 -377
  53. package/skills/autoskill/config.yaml +0 -53
  54. package/skills/autoskill/references/https-proxy.md +0 -62
  55. package/skills/autoskill/references/screenpipe-config.yaml +0 -61
  56. package/skills/autoskill/scripts/autoskill.py +0 -35
  57. package/skills/autoskill/scripts/backends.py +0 -116
  58. package/skills/autoskill/scripts/cluster.py +0 -54
  59. package/skills/autoskill/scripts/doctor.py +0 -108
  60. package/skills/autoskill/scripts/fetch_window.py +0 -33
  61. package/skills/autoskill/scripts/match_skills.py +0 -46
  62. package/skills/autoskill/scripts/promote.py +0 -58
  63. package/skills/autoskill/scripts/redact.py +0 -40
  64. package/skills/autoskill/scripts/run.py +0 -194
  65. package/skills/autoskill/scripts/synthesize.py +0 -72
  66. package/skills/benchling-integration/references/api_endpoints.md +0 -883
  67. package/skills/benchling-integration/references/authentication.md +0 -390
  68. package/skills/benchling-integration/references/core_capabilities.md +0 -355
  69. package/skills/benchling-integration/references/eventbridge.md +0 -255
  70. package/skills/benchling-integration/references/sdk_reference.md +0 -772
  71. package/skills/bids/references/beps.yml +0 -637
  72. package/skills/bids/references/bids_schema.json +0 -21015
  73. package/skills/bids/references/bids_specification.md +0 -165
  74. package/skills/bids/references/conversion_tools.md +0 -475
  75. package/skills/bids/references/core_workflows.md +0 -552
  76. package/skills/bids/references/metadata_fields.md +0 -365
  77. package/skills/bids/scripts/update_schema.py +0 -89
  78. package/skills/biopython/references/advanced.md +0 -580
  79. package/skills/biopython/references/alignment.md +0 -377
  80. package/skills/biopython/references/blast.md +0 -463
  81. package/skills/biopython/references/databases.md +0 -492
  82. package/skills/biopython/references/phylogenetics.md +0 -566
  83. package/skills/biopython/references/sequence_io.md +0 -289
  84. package/skills/biopython/references/structure.md +0 -564
  85. package/skills/bioservices/references/identifier_mapping.md +0 -685
  86. package/skills/bioservices/references/services_reference.md +0 -638
  87. package/skills/bioservices/references/workflow_patterns.md +0 -813
  88. package/skills/bioservices/scripts/batch_id_converter.py +0 -347
  89. package/skills/bioservices/scripts/compound_cross_reference.py +0 -387
  90. package/skills/bioservices/scripts/pathway_analysis.py +0 -309
  91. package/skills/bioservices/scripts/protein_analysis_workflow.py +0 -441
  92. package/skills/bulk-rnaseq/references/counts-and-handoff.md +0 -91
  93. package/skills/bulk-rnaseq/references/design-and-qc.md +0 -68
  94. package/skills/bulk-rnaseq/references/upstream-manual.md +0 -128
  95. package/skills/bulk-rnaseq/references/upstream-nfcore.md +0 -108
  96. package/skills/bulk-rnaseq/scripts/build_counts_matrix.py +0 -203
  97. package/skills/bulk-rnaseq/scripts/validate_samplesheet.py +0 -206
  98. package/skills/cellxgene-census/references/census_schema.md +0 -218
  99. package/skills/cellxgene-census/references/common_patterns.md +0 -368
  100. package/skills/cellxgene-census/references/core_workflow_patterns.md +0 -297
  101. package/skills/cirq/references/building.md +0 -307
  102. package/skills/cirq/references/experiments.md +0 -572
  103. package/skills/cirq/references/hardware.md +0 -527
  104. package/skills/cirq/references/noise.md +0 -514
  105. package/skills/cirq/references/simulation.md +0 -353
  106. package/skills/cirq/references/transformation.md +0 -416
  107. package/skills/citation-management/assets/bibtex_template.bib +0 -264
  108. package/skills/citation-management/assets/citation_checklist.md +0 -386
  109. package/skills/citation-management/references/best_practices.md +0 -91
  110. package/skills/citation-management/references/bibtex_formatting.md +0 -908
  111. package/skills/citation-management/references/citation_validation.md +0 -835
  112. package/skills/citation-management/references/core_workflow.md +0 -569
  113. package/skills/citation-management/references/example_workflows.md +0 -126
  114. package/skills/citation-management/references/google_scholar_search.md +0 -732
  115. package/skills/citation-management/references/metadata_extraction.md +0 -870
  116. package/skills/citation-management/references/pubmed_search.md +0 -839
  117. package/skills/citation-management/references/script_reference.md +0 -250
  118. package/skills/citation-management/references/search_strategies.md +0 -110
  119. package/skills/citation-management/scripts/_common.py +0 -331
  120. package/skills/citation-management/scripts/doi_to_bibtex.py +0 -204
  121. package/skills/citation-management/scripts/extract_metadata.py +0 -690
  122. package/skills/citation-management/scripts/format_bibtex.py +0 -356
  123. package/skills/citation-management/scripts/search_google_scholar.py +0 -268
  124. package/skills/citation-management/scripts/search_openalex.py +0 -297
  125. package/skills/citation-management/scripts/search_pubmed.py +0 -419
  126. package/skills/citation-management/scripts/validate_citations.py +0 -688
  127. package/skills/clinical-decision-support/assets/aggregate_cohort_table_template.json +0 -114
  128. package/skills/clinical-decision-support/assets/aggregate_model_evaluation_template.json +0 -115
  129. package/skills/clinical-decision-support/assets/artifact_intended_use_template.json +0 -81
  130. package/skills/clinical-decision-support/assets/decision_logic_traceability_template.json +0 -108
  131. package/skills/clinical-decision-support/assets/deidentification_checklist_template.json +0 -176
  132. package/skills/clinical-decision-support/assets/evidence_profile_template.json +0 -139
  133. package/skills/clinical-decision-support/assets/survival_analysis_plan_template.json +0 -134
  134. package/skills/clinical-decision-support/references/cohort_evaluation.md +0 -142
  135. package/skills/clinical-decision-support/references/decision_logic_traceability.md +0 -146
  136. package/skills/clinical-decision-support/references/evidence_profiles.md +0 -153
  137. package/skills/clinical-decision-support/references/model_biomarker_evaluation.md +0 -152
  138. package/skills/clinical-decision-support/references/privacy_and_disclosure.md +0 -144
  139. package/skills/clinical-decision-support/references/regulatory_and_governance.md +0 -104
  140. package/skills/clinical-decision-support/references/safety_and_scope.md +0 -103
  141. package/skills/clinical-decision-support/references/security_validation.md +0 -60
  142. package/skills/clinical-decision-support/references/sources.md +0 -119
  143. package/skills/clinical-decision-support/references/study_reporting.md +0 -134
  144. package/skills/clinical-decision-support/references/survival_analysis.md +0 -156
  145. package/skills/clinical-decision-support/scripts/_common.py +0 -223
  146. package/skills/clinical-decision-support/scripts/cohort_table_generator.py +0 -288
  147. package/skills/clinical-decision-support/scripts/decision_logic_traceability.py +0 -313
  148. package/skills/clinical-decision-support/scripts/deidentification_checklist.py +0 -260
  149. package/skills/clinical-decision-support/scripts/evidence_profile_check.py +0 -259
  150. package/skills/clinical-decision-support/scripts/model_biomarker_evaluation.py +0 -345
  151. package/skills/clinical-decision-support/scripts/survival_plan_validator.py +0 -294
  152. package/skills/clinical-decision-support/scripts/validate_cds_artifact.py +0 -269
  153. package/skills/clinical-reports/assets/adverse_event_aggregate_input_template.csv +0 -1
  154. package/skills/clinical-reports/assets/case_report_template.json +0 -43
  155. package/skills/clinical-reports/assets/clinical_trial_csr_template.json +0 -51
  156. package/skills/clinical-reports/assets/clinical_trial_results_template.json +0 -66
  157. package/skills/clinical-reports/assets/clinical_trial_safety_aggregate_template.json +0 -49
  158. package/skills/clinical-reports/assets/consistency_manifest_template.json +0 -15
  159. package/skills/clinical-reports/assets/deidentification_process_checklist.json +0 -56
  160. package/skills/clinical-reports/assets/lab_report_template.json +0 -36
  161. package/skills/clinical-reports/assets/pathology_report_template.json +0 -36
  162. package/skills/clinical-reports/assets/provenance_manifest_template.json +0 -17
  163. package/skills/clinical-reports/assets/quality_review_checklist.json +0 -34
  164. package/skills/clinical-reports/assets/radiology_report_template.json +0 -34
  165. package/skills/clinical-reports/assets/research_summary_template.json +0 -36
  166. package/skills/clinical-reports/assets/terminology_manifest_template.json +0 -11
  167. package/skills/clinical-reports/assets/trial_protocol_reporting_checklist.json +0 -70
  168. package/skills/clinical-reports/references/case_report_guidelines.md +0 -72
  169. package/skills/clinical-reports/references/clinical_trial_reporting.md +0 -97
  170. package/skills/clinical-reports/references/data_presentation.md +0 -92
  171. package/skills/clinical-reports/references/diagnostic_reports_standards.md +0 -76
  172. package/skills/clinical-reports/references/medical_terminology.md +0 -84
  173. package/skills/clinical-reports/references/privacy_and_deidentification.md +0 -84
  174. package/skills/clinical-reports/references/professional_review.md +0 -78
  175. package/skills/clinical-reports/references/report_type_routing.md +0 -57
  176. package/skills/clinical-reports/references/safety_reporting.md +0 -109
  177. package/skills/clinical-reports/references/sources.md +0 -75
  178. package/skills/clinical-reports/scripts/_common.py +0 -263
  179. package/skills/clinical-reports/scripts/check_deidentification.py +0 -298
  180. package/skills/clinical-reports/scripts/consistency_checker.py +0 -390
  181. package/skills/clinical-reports/scripts/format_adverse_events.py +0 -455
  182. package/skills/clinical-reports/scripts/generate_report_template.py +0 -115
  183. package/skills/clinical-reports/scripts/provenance_validator.py +0 -263
  184. package/skills/clinical-reports/scripts/terminology_validator.py +0 -277
  185. package/skills/clinical-reports/scripts/validate_case_report.py +0 -278
  186. package/skills/clinical-reports/scripts/validate_trial_report.py +0 -534
  187. package/skills/cobrapy/references/api_quick_reference.md +0 -665
  188. package/skills/cobrapy/references/workflows.md +0 -600
  189. package/skills/consciousness-council/references/advanced-configurations.md +0 -96
  190. package/skills/dask/references/arrays.md +0 -495
  191. package/skills/dask/references/bags.md +0 -468
  192. package/skills/dask/references/best-practices.md +0 -277
  193. package/skills/dask/references/dataframes.md +0 -370
  194. package/skills/dask/references/futures.md +0 -541
  195. package/skills/dask/references/schedulers.md +0 -517
  196. package/skills/database-lookup/references/addgene.md +0 -38
  197. package/skills/database-lookup/references/alphafold.md +0 -52
  198. package/skills/database-lookup/references/alphavantage.md +0 -261
  199. package/skills/database-lookup/references/bea.md +0 -409
  200. package/skills/database-lookup/references/bindingdb.md +0 -85
  201. package/skills/database-lookup/references/biogrid.md +0 -110
  202. package/skills/database-lookup/references/bls.md +0 -235
  203. package/skills/database-lookup/references/brenda.md +0 -71
  204. package/skills/database-lookup/references/cbioportal.md +0 -206
  205. package/skills/database-lookup/references/census.md +0 -251
  206. package/skills/database-lookup/references/chebi.md +0 -103
  207. package/skills/database-lookup/references/chembl.md +0 -80
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  212. package/skills/database-lookup/references/cosmic.md +0 -59
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  218. package/skills/database-lookup/references/drugbank.md +0 -54
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  221. package/skills/database-lookup/references/ena.md +0 -372
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  229. package/skills/database-lookup/references/gene-ontology.md +0 -147
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  236. package/skills/database-lookup/references/human-protein-atlas.md +0 -57
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@@ -1,264 +0,0 @@
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- # Evaluation Framework
2
-
3
- ## What ScholarEval is—and is not
4
-
5
- The paper currently referenced by this skill is Moussa et al.,
6
- [*ScholarEval: Research Idea Evaluation Grounded in
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- Literature*](https://arxiv.org/abs/2510.16234), arXiv:2510.16234v2,
8
- revised 2026-02-28.
9
-
10
- The preprint describes an experimental retrieval-augmented system for evaluating
11
- research ideas on:
12
-
13
- - **soundness:** whether existing literature empirically supports proposed
14
- methods; and
15
- - **contribution:** how an idea advances beyond prior work along comparison
16
- dimensions.
17
-
18
- It reports a 117-idea, four-discipline dataset, coverage comparisons with
19
- expert-annotated review points, and a user study. Those studies evaluate that
20
- framework. They do **not** validate the generalized rubric in this skill as a
21
- psychometric instrument, establish stable score meaning across disciplines, or
22
- authorize use in consequential decisions.
23
-
24
- As of the dated source review, arXiv and the official project repository were
25
- the verified primary publication records. No peer-reviewed publication status
26
- was verified. Cite it as an arXiv preprint unless a later primary record is
27
- checked. See `references/source_ledger.md`.
28
-
29
- ## Relationship to this skill
30
-
31
- This skill borrows the useful discipline of:
32
-
33
- 1. defining what is being assessed;
34
- 2. grounding judgments in traceable literature and work evidence;
35
- 3. separating soundness-like questions from contribution-like questions; and
36
- 4. auditing whether generated feedback covers expert concerns.
37
-
38
- It does not reproduce ScholarEval's model pipeline, prompts, retrieval system,
39
- dataset, or reported metrics. The bundled scripts do not call ScholarEval,
40
- search the web, invoke a model, or evaluate private documents.
41
-
42
- The template is a **locally governed developmental rubric**. Its default
43
- construct is:
44
-
45
- > Traceable support for a scholarly work's claims and methods: the degree to
46
- > which a work states a bounded question, situates its contribution, uses
47
- > fit-for-purpose methods, aligns analysis with claims, and documents
48
- > transparent and responsible practices using traceable evidence.
49
-
50
- This construct must be reviewed and adapted by relevant disciplinary experts.
51
-
52
- ## Five template criteria
53
-
54
- ### 1. Question and scope
55
-
56
- Review:
57
-
58
- - a clear, bounded question or objective;
59
- - significance rationale appropriate to the field and work stage;
60
- - assumptions, boundary conditions, and success conditions; and
61
- - feasibility of the proposed or reported scope.
62
-
63
- Do not treat fashionable topics, institutional affiliation, or venue
64
- expectations as evidence of significance.
65
-
66
- ### 2. Literature grounding and contribution claim
67
-
68
- Review:
69
-
70
- - source-selection or search boundaries;
71
- - engagement with relevant and contrary evidence;
72
- - traceable primary sources for comparison claims;
73
- - comparison dimensions used to define the contribution; and
74
- - limits on novelty or advancement claims.
75
-
76
- Failure to find prior work does not establish novelty. Search coverage varies by
77
- database, language, date, indexing, terminology, discipline, and access.
78
-
79
- ### 3. Method and design fit
80
-
81
- Review:
82
-
83
- - alignment between question, design, data or materials, and method;
84
- - sampling, corpus, inclusion, exclusion, and measurement choices;
85
- - alternatives and design rationale;
86
- - validity threats, bias, and mitigation;
87
- - ethics, consent, privacy, safety, and governance; and
88
- - detail sufficient for appropriate checking or reproduction.
89
-
90
- Use discipline-specific reporting and methods standards. Do not reward
91
- complexity for its own sake.
92
-
93
- ### 4. Analysis, claims, and uncertainty
94
-
95
- Review:
96
-
97
- - fit of analytical methods to data and inferential target;
98
- - assumptions and diagnostics;
99
- - robustness, sensitivity, negative cases, and alternative explanations;
100
- - appropriate statistical or qualitative uncertainty;
101
- - alignment between results and claims; and
102
- - explicit limits on generalization and causal language.
103
-
104
- The rubric's `uncertainty` value is a rater-supplied bounded judgment range. It
105
- is not a sampling confidence interval, posterior interval, or standard error.
106
-
107
- ### 5. Transparency, integrity, and reproducibility
108
-
109
- Review:
110
-
111
- - complete reporting, provenance, and stable evidence locators;
112
- - protocols, registrations, data, code, materials, and justified restrictions;
113
- - negative, null, and contradictory findings where relevant;
114
- - conflicts, limitations, corrections, and research-integrity safeguards;
115
- - accessible communication; and
116
- - transparent attribution of contributions.
117
-
118
- Open practice is not an absolute requirement when privacy, consent, safety,
119
- security, Indigenous data governance, commercial constraints, or other
120
- legitimate restrictions apply. Assess whether restrictions are justified and
121
- whether safe access or metadata alternatives are provided.
122
-
123
- ## Scale semantics
124
-
125
- The template uses an ordinal 0–4 scale:
126
-
127
- - **0 — no assessable evidence**
128
- - **1 — limited support**
129
- - **2 — mixed support**
130
- - **3 — substantial support**
131
- - **4 — strong support**
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-
133
- These are evidence anchors, not labels of a person or universal levels of
134
- research quality. The rubric defines criterion-specific anchors. Raters must use
135
- the anchor text, not intuition about what a number “usually means.”
136
-
137
- Do not convert the score to:
138
-
139
- - accept/reject or publication readiness;
140
- - exceptional/poor labels;
141
- - predicted success or impact;
142
- - person ranking; or
143
- - funding, hiring, promotion, tenure, admissions, award, or discipline advice.
144
-
145
- ## Rating statuses
146
-
147
- Each criterion has exactly one status:
148
-
149
- - `rated`: score, uncertainty, evidence identifiers, and rationale reference
150
- are required;
151
- - `missing`: evidence needed for assessment is absent or unavailable; score and
152
- uncertainty are null; or
153
- - `not_applicable`: the criterion does not apply to this work under a documented
154
- rationale; score and uncertainty are null.
155
-
156
- Do not encode missing or not-applicable as zero.
157
-
158
- ## Transparent score math
159
-
160
- For rated criteria \(R\), score \(s_i\), and predeclared weight \(w_i\):
161
-
162
- \[
163
- \text{descriptive score}
164
- =
165
- \frac{\sum_{i \in R} w_i s_i}
166
- {\sum_{i \in R} w_i}
167
- \]
168
-
169
- The score report separately provides:
170
-
171
- - total, applicable, rated, missing, and not-applicable weight;
172
- - coverage of applicable weight;
173
- - each weighted contribution;
174
- - the normalized descriptive score; and
175
- - a bounded aggregation of criterion uncertainty ranges.
176
-
177
- The uncertainty aggregation is not a confidence interval. Normalization does
178
- not make incomplete evaluations comparable. Review missingness before looking
179
- at any score.
180
-
181
- ## Rubric development record
182
-
183
- Before replacing `content_validity_status: not_established`, document:
184
-
185
- 1. the exact discipline, work type, language, stage, and intended use;
186
- 2. construct definition and excluded constructs;
187
- 3. literature and standard review used to draft criteria;
188
- 4. disciplinary expert and stakeholder selection;
189
- 5. systematic mapping of criteria to construct components;
190
- 6. cognitive interviews or rater response-process evidence;
191
- 7. accessibility and translation review;
192
- 8. pilot sample and evidence-availability analysis;
193
- 9. revisions, dissent, unresolved gaps, and approval; and
194
- 10. the limits of any validity claim.
195
-
196
- Rubric provenance must identify the version, owner role, source identifiers,
197
- review date, and content-evidence reference.
198
-
199
- ## Rater protocol
200
-
201
- At minimum:
202
-
203
- 1. select qualified raters with relevant disciplinary and methods expertise;
204
- 2. disclose conflicts and recuse where required;
205
- 3. train on construct boundaries, anchors, evidence rules, missingness,
206
- accessibility, bias, and privacy;
207
- 4. calibrate on synthetic or authorized examples;
208
- 5. rate independently before discussion;
209
- 6. record evidence identifiers and uncertainty;
210
- 7. summarize agreement and investigate systematic disagreements;
211
- 8. resolve only through documented evidence and rationale, not forced averaging;
212
- 9. monitor drift over time; and
213
- 10. retrain, revise, or suspend the rubric when evidence warrants.
214
-
215
- The bundled agreement script reports exact agreement, within-one-step agreement,
216
- and mean absolute difference. Those summaries do not replace a
217
- design-appropriate reliability analysis. The rubric therefore separately
218
- records `inter_rater_reliability_status` and
219
- `inter_rater_reliability_ref`; the template leaves reliability not established.
220
-
221
- ## Evidence traceability
222
-
223
- Each rated criterion must point to one or more entries in the evidence manifest.
224
- Each entry records:
225
-
226
- - pseudonymous evidence identifier;
227
- - linked criterion identifiers;
228
- - source type;
229
- - local stable locator;
230
- - local claim reference;
231
- - access status; and
232
- - verification status.
233
-
234
- Never place an excerpt or raw private document in the manifest. Keep source
235
- content in the authorized source system.
236
-
237
- ## Weight sensitivity and order instability
238
-
239
- Weights are value judgments. Predeclare and justify them. Run
240
- `scripts/weight_sensitivity.py` before interpreting a composite.
241
-
242
- The script increases and decreases one weight at a time and renormalizes the
243
- weights. It reports score ranges and whether pairwise ordinal relationships
244
- among scholarly works change. Instability is evidence that an apparent order
245
- depends on contestable weights.
246
-
247
- The output must not be used to rank people or decide a high-impact outcome.
248
- Even stable ordering does not establish validity.
249
-
250
- ## Interpretation template
251
-
252
- For each criterion, qualified reviewers should record:
253
-
254
- 1. status and evidence references;
255
- 2. observed evidence;
256
- 3. interpretation against the anchor;
257
- 4. score and uncertainty, if rated;
258
- 5. missing or not-applicable rationale;
259
- 6. disciplinary and stage context;
260
- 7. strengths and limitations; and
261
- 8. non-prescriptive improvement options.
262
-
263
- Conclude with construct, provenance, coverage, agreement, sensitivity, bias,
264
- privacy, accessibility, and validity limitations—not a decision recommendation.
@@ -1,232 +0,0 @@
1
- # Local Deterministic Tooling
2
-
3
- ## Security properties
4
-
5
- Every bundled script:
6
-
7
- - uses only the Python standard library;
8
- - reads bounded local `.json` or `.csv` files;
9
- - rejects symbolic-link inputs, duplicate JSON keys, excessive depth or size,
10
- non-finite numbers, unknown schema fields, and common private-application
11
- fields;
12
- - uses fixed schemas and never executes supplied text;
13
- - has no network, model, credential, environment-file, dynamic-code,
14
- executable-serialization, or child-process behavior;
15
- - writes only minimized JSON reports and refuses to overwrite by default; and
16
- - does not copy evidence excerpts or raw source documents.
17
-
18
- Inputs are limited to 2 MiB, JSON depth 20, 25,000 structure nodes, 50 rubric
19
- criteria, 50 comparison evaluations, and 20,000 agreement rows. Outputs are
20
- limited to 2 MiB.
21
-
22
- Use an authorized local directory. Keep private source documents in the
23
- institution's records system and reference them with opaque local identifiers.
24
-
25
- ## Templates
26
-
27
- - `assets/rubric_template.json` — valid structure, but deliberately records
28
- content validity as not established.
29
- - `assets/evaluation_template.json` — structurally valid all-missing example.
30
- - `assets/evidence_manifest_template.json` — synthetic local-reference records.
31
- - `assets/process_checklist_template.json` — fail-closed unconfirmed controls.
32
- - `assets/ratings_template.csv` — pseudonymous synthetic agreement data.
33
-
34
- Copy a template into an authorized working directory before editing it. Do not
35
- replace synthetic identifiers with names or contact information.
36
-
37
- ## 1. Rubric schema validation
38
-
39
- ```bash
40
- PYTHONDONTWRITEBYTECODE=1 python3 scripts/validate_rubric.py \
41
- --rubric assets/rubric_template.json
42
- ```
43
-
44
- The validator checks:
45
-
46
- - fixed intended use and scholarly-work unit;
47
- - complete prohibited-use list;
48
- - construct, boundaries, limitations, and provenance;
49
- - content-validity status and reference;
50
- - bounded scale and complete anchors;
51
- - unique criteria and weights summing to one;
52
- - absence of common scored proxy measures;
53
- - required rater training, calibration, agreement, separately recorded
54
- inter-rater reliability status, and drift controls; and
55
- - committee, conflict, appeal, accessibility, data-protection, subgroup, and
56
- review-cycle governance.
57
-
58
- A rubric can be structurally `valid` while warning that content validity is not
59
- documented. Structural validity is not psychometric validity.
60
-
61
- ## 2. Bounded descriptive scoring
62
-
63
- ```bash
64
- PYTHONDONTWRITEBYTECODE=1 python3 scripts/calculate_scores.py \
65
- --rubric assets/rubric_template.json \
66
- --evaluation assets/evaluation_template.json \
67
- --output /tmp/scholar-score.json
68
- ```
69
-
70
- The evaluation contains one entry for every criterion:
71
-
72
- ```json
73
- {
74
- "criterion_id": "method_design",
75
- "status": "rated",
76
- "score": 3,
77
- "uncertainty": 0.5,
78
- "evidence_ids": ["EVIDENCE-SYNTHETIC-METHOD"],
79
- "rationale_ref": "LOCAL-RATING-RATIONALE-METHOD"
80
- }
81
- ```
82
-
83
- For `missing` or `not_applicable`, `score` and `uncertainty` must be null and
84
- `evidence_ids` must be empty. A local rationale reference remains required.
85
-
86
- The output reports weighted contributions, coverage, missing and
87
- not-applicable weight, normalized score, and a bounded uncertainty range. It
88
- contains no quality label, threshold, decision, or recommendation.
89
-
90
- ## 3. Evidence traceability
91
-
92
- ```bash
93
- PYTHONDONTWRITEBYTECODE=1 python3 scripts/check_traceability.py \
94
- --rubric assets/rubric_template.json \
95
- --evaluation assets/evaluation_template.json \
96
- --evidence assets/evidence_manifest_template.json
97
- ```
98
-
99
- The checker verifies that:
100
-
101
- - manifest, evaluation, work, and classification identifiers match;
102
- - every evidence identifier is unique;
103
- - every rated evidence reference resolves;
104
- - evidence is linked to the criterion that cites it;
105
- - source and access types are allowed; and
106
- - evidence is available and verified.
107
-
108
- It reports identifiers, paths, and counts only. It never opens or copies the
109
- referenced source.
110
-
111
- ## 4. Weight sensitivity and rank instability
112
-
113
- Provide two to 50 evaluation JSON files for distinct scholarly works:
114
-
115
- ```bash
116
- PYTHONDONTWRITEBYTECODE=1 python3 scripts/weight_sensitivity.py \
117
- --rubric assets/rubric_template.json \
118
- --evaluation /tmp/work-a-evaluation.json \
119
- --evaluation /tmp/work-b-evaluation.json \
120
- --delta 0.2 \
121
- --output /tmp/weight-sensitivity.json
122
- ```
123
-
124
- For each criterion, the script multiplies its weight by `1-delta` and
125
- `1+delta`, renormalizes all weights to one, and recomputes descriptive scores.
126
- It reports:
127
-
128
- - every scenario and its exact weights;
129
- - each work's score and coverage per scenario;
130
- - score ranges;
131
- - base ordinal order; and
132
- - pairwise order changes.
133
-
134
- The base order is included solely to detect instability. It is not a ranking
135
- recommendation and must never be used for people or high-impact decisions.
136
-
137
- ## 5. Inter-rater agreement summaries
138
-
139
- The CSV header must be exactly:
140
-
141
- ```text
142
- evaluation_id,work_id,rater_id,criterion_id,status,score
143
- ```
144
-
145
- Use pseudonymous rater identifiers. Run:
146
-
147
- ```bash
148
- PYTHONDONTWRITEBYTECODE=1 python3 scripts/summarize_agreement.py \
149
- --rubric assets/rubric_template.json \
150
- --ratings assets/ratings_template.csv \
151
- --output /tmp/agreement-summary.json
152
- ```
153
-
154
- For each criterion and overall, the report includes:
155
-
156
- - pair observations;
157
- - exact agreement rate;
158
- - within-one-scale-step agreement rate;
159
- - mean absolute difference;
160
- - overlap, rated, missing, and not-applicable counts.
161
-
162
- Rater identifiers are not emitted. These are descriptive agreement summaries,
163
- not chance-corrected reliability, generalizability, validity, or fairness
164
- evidence.
165
-
166
- ## 6. Bias and process checklist
167
-
168
- ```bash
169
- PYTHONDONTWRITEBYTECODE=1 python3 scripts/check_process.py \
170
- --process assets/process_checklist_template.json
171
- ```
172
-
173
- The template is intentionally unconfirmed and therefore does not pass. Complete
174
- it only from documented local records. The checker covers:
175
-
176
- - qualified committee and training;
177
- - conflicts and recusal;
178
- - appeal and correction;
179
- - accessibility and accommodations;
180
- - purpose limitation, minimization, access, retention, and output controls;
181
- - construct, provenance, content evidence, rater quality, agreement,
182
- inter-rater reliability review, uncertainty, missingness, traceability, and
183
- sensitivity;
184
- - stakeholder, disciplinary, subgroup, and protected-attribute safeguards;
185
- - no automation, person ranking, or decision recommendation; and
186
- - drift, unintended-consequence, and periodic review.
187
-
188
- `high_impact_use: true` or any unconfirmed decision control blocks the process.
189
- The checklist does not authorize a prohibited use.
190
-
191
- ## 7. Report scaffold
192
-
193
- Generate a minimized scaffold:
194
-
195
- ```bash
196
- PYTHONDONTWRITEBYTECODE=1 python3 scripts/generate_report_scaffold.py \
197
- --rubric assets/rubric_template.json \
198
- --evaluation assets/evaluation_template.json \
199
- --output /tmp/developmental-report-scaffold.json
200
- ```
201
-
202
- Optional companion reports:
203
-
204
- ```bash
205
- PYTHONDONTWRITEBYTECODE=1 python3 scripts/generate_report_scaffold.py \
206
- --rubric assets/rubric_template.json \
207
- --evaluation /tmp/work-a-evaluation.json \
208
- --traceability /tmp/traceability.json \
209
- --agreement /tmp/agreement-summary.json \
210
- --sensitivity /tmp/weight-sensitivity.json \
211
- --process /tmp/process-check.json \
212
- --output /tmp/developmental-report-scaffold.json
213
- ```
214
-
215
- The scaffold includes:
216
-
217
- - construct and provenance status;
218
- - descriptive scores and uncertainty;
219
- - empty local-reference slots for evidence, strengths, limitations, and
220
- improvement options;
221
- - minimized quality-assurance statuses; and
222
- - fixed limitations and human-review fields.
223
-
224
- It does not draft findings from source documents or issue a decision.
225
-
226
- ## Exit behavior
227
-
228
- - exit `0`: requested calculation or validation completed successfully;
229
- - exit `2`: invalid, blocked, incomplete, failed traceability, or unsafe input.
230
-
231
- Errors contain only stable codes and JSON paths, never supplied values. Use
232
- `--force` only when replacing a known local report.
@@ -1,196 +0,0 @@
1
- # Responsible Assessment and Safety Boundary
2
-
3
- ## Non-negotiable boundary
4
-
5
- This skill is for **developmental review of scholarly works** and for auditing a
6
- low-stakes assessment process. It must not automate, recommend, materially
7
- influence, or provide a score for:
8
-
9
- - hiring, promotion, or tenure;
10
- - admissions;
11
- - grant or other funding decisions;
12
- - prizes, honors, or awards;
13
- - discipline, dismissal, or sanctions; or
14
- - any other high-impact personnel decision.
15
-
16
- Do not rank people. Do not convert several judgments into a single composite
17
- person score. Do not infer a person's ability, character, integrity, future
18
- performance, protected characteristics, or institutional worth.
19
-
20
- This boundary remains in force when a human is nominally “in the loop.”
21
- Checklists, committees, or disclaimers do not make a prohibited workflow safe.
22
- If a request crosses the boundary, stop and offer one of these alternatives:
23
-
24
- 1. developmental comments on a public or authorized scholarly work, with no
25
- person comparison or decision advice;
26
- 2. an audit of whether an existing assessment process follows responsible
27
- assessment principles, without processing applications or recommending an
28
- outcome; or
29
- 3. neutral documentation of criteria for review by the organization's legal,
30
- privacy, accessibility, labor, ethics, and disciplinary experts.
31
-
32
- ## Allowed scope
33
-
34
- Examples of allowed uses, subject to authorization and data protection:
35
-
36
- - feedback on a draft paper, protocol, research idea, or literature synthesis;
37
- - a retrospective methods or reporting review;
38
- - calibration exercises using synthetic or public scholarly works;
39
- - checking evidence traceability;
40
- - describing the sensitivity of work-level scores to rubric weights; and
41
- - auditing a low-stakes evaluation design for missing governance controls.
42
-
43
- “Publication readiness” and “accept/reject” recommendations are excluded.
44
- Describe evidence, limitations, and improvement options instead.
45
-
46
- ## Accountable human process
47
-
48
- For any organizational use, an accountable committee must own the process. It
49
- must include relevant disciplinary and assessment-methods expertise and must:
50
-
51
- - publish the construct, intended use, rubric, weights, evidence requirements,
52
- and interpretation limits before reviewing;
53
- - record member qualifications, training, calibration, and drift checks;
54
- - disclose conflicts, require recusal, and maintain a conflict record;
55
- - provide an understandable notice and a meaningful appeal or correction route;
56
- - provide accessible materials and reasonable accommodations;
57
- - define lawful purpose, access controls, minimization, retention, and deletion;
58
- - review disciplinary, language, career-path, disability, and subgroup effects;
59
- - document disagreements and uncertainty rather than force consensus; and
60
- - periodically evaluate and revise the evaluation.
61
-
62
- No script in this skill is the accountable reviewer. Script output is a
63
- descriptive record for qualified human interpretation.
64
-
65
- ## Qualitative-first evidence
66
-
67
- Start with the values and construct, not the data that happen to be available.
68
- Use evidence that directly bears on the criterion:
69
-
70
- - the work's questions, methods, analyses, outputs, limitations, and provenance;
71
- - datasets, software, protocols, materials, registrations, replications, and
72
- negative or null findings where relevant;
73
- - transparent records of responsible practices and justified restrictions;
74
- - contribution records, including CRediT roles when useful, without treating a
75
- role as proof of quality; and
76
- - influence on policy, practice, communities, teaching, infrastructure, or
77
- knowledge, when this is within the stated construct and supported by evidence.
78
-
79
- Ask what is missing, inaccessible, contested, or not applicable. A missing item
80
- is not a zero. A not-applicable item is not evidence of deficiency.
81
-
82
- ## Prohibited proxies and contextual indicators
83
-
84
- Do not score or infer quality from:
85
-
86
- - Journal Impact Factor or other journal-level measures;
87
- - h-index, i10-index, publication counts, or citation counts;
88
- - altmetrics or attention counts;
89
- - journal, conference, institutional, geographic, or employer prestige;
90
- - venue identity or ranking; or
91
- - author affiliation, career path, network, or reputation.
92
-
93
- The bundled rubric validator rejects common proxy-measure criteria.
94
-
95
- If a qualified reviewer has a legitimate, predeclared reason to mention a
96
- quantitative indicator descriptively outside the bundled scoring tools, record:
97
-
98
- 1. the exact construct and purpose;
99
- 2. why the indicator bears on that construct at the correct unit of analysis;
100
- 3. source, version, query date, coverage, exclusions, and data quality;
101
- 4. field, language, output-type, career-stage, and time-window effects;
102
- 5. uncertainty, missingness, gaming risks, and known biases;
103
- 6. why qualitative evidence is insufficient by itself; and
104
- 7. a statement that the indicator is not a direct measure of quality.
105
-
106
- Never use an indicator merely because it is available. Never hide several
107
- different indicators inside an opaque composite.
108
-
109
- ## Rubric evidence and psychometric caution
110
-
111
- A rubric is a measurement claim. Before operational use, record:
112
-
113
- - **construct:** what is and is not being assessed;
114
- - **intended interpretation and use:** the exact meaning claimed for scores;
115
- - **provenance:** who designed and approved criteria, anchors, and weights;
116
- - **content evidence:** disciplinary expert and stakeholder review of coverage;
117
- - **response process:** how raters interpret anchors and use evidence;
118
- - **rater protocol:** selection, training, calibration, qualification, and drift;
119
- - **agreement/reliability:** a design-appropriate analysis and its uncertainty;
120
- - **fairness:** accessibility, subgroup, language, and disciplinary review;
121
- - **traceability:** stable evidence references for each rating;
122
- - **missing/not applicable:** explicit statuses and rationales;
123
- - **weight sensitivity:** whether plausible weights change descriptive results;
124
- - **consequences:** gaming, burden, goal displacement, and other effects; and
125
- - **revision:** review date, owner, change record, and retirement criteria.
126
-
127
- Do not call a rubric “validated” because experts reviewed it once, raters agreed,
128
- or scores correlated with another judgment. Validity concerns the evidence for a
129
- specific interpretation and use. Reliability or agreement alone is not validity.
130
-
131
- The provided rubric explicitly records `content_validity_status` as
132
- `not_established`. Replace that status only when a qualified team has documented
133
- appropriate evidence for the exact discipline, population, language, and use.
134
-
135
- ## Bias and subgroup review
136
-
137
- Perform the fairness review outside these scripts in an authorized environment.
138
- Do not place protected-attribute records in rubric, evaluation, evidence, or
139
- ratings files.
140
-
141
- A qualified review should examine, where lawful and appropriate:
142
-
143
- - access to the measured construct and accommodation effectiveness;
144
- - differential missingness and evidence availability;
145
- - criteria that privilege particular languages, methods, fields, institutions,
146
- career patterns, or resource levels;
147
- - rater severity, drift, and disagreement patterns;
148
- - differential effects of weights and not-applicable decisions;
149
- - false precision and threshold effects;
150
- - burden, gaming, and chilling of collaboration or risky research; and
151
- - whether the evaluation should be redesigned or stopped.
152
-
153
- Report sample limitations and uncertainty. Do not expose small cells or attempt
154
- to infer sensitive characteristics.
155
-
156
- ## Privacy and data protection
157
-
158
- Use only public scholarly works, synthetic records, or deidentified low-stakes
159
- records processed under an approved local purpose. Do not put raw private
160
- applications, CVs, recommendation letters, reviewer identities, contact
161
- details, protected attributes, or source-document text into tool inputs or
162
- outputs.
163
-
164
- The bundled formats contain only:
165
-
166
- - pseudonymous work, evaluation, rater, criterion, and evidence identifiers;
167
- - bounded scores, statuses, and uncertainty;
168
- - local stable references; and
169
- - minimized control attestations and aggregate summaries.
170
-
171
- Keep source documents in the authorized records system. Use local references to
172
- them. Apply least privilege, retention limits, deletion, incident handling, and
173
- any stricter local law or policy.
174
-
175
- ## Accessibility
176
-
177
- Provide the rubric, evidence requirements, notices, feedback, and appeal
178
- process in accessible formats. Do not penalize an accommodation, assistive
179
- technology, language variant, or accessible presentation choice. Confirm that
180
- the rubric measures the intended construct rather than fluency with an
181
- inaccessible interface or format.
182
-
183
- ## Communicating results
184
-
185
- Lead with qualitative, traceable findings. For every criterion:
186
-
187
- 1. cite local evidence references;
188
- 2. state the rating status;
189
- 3. distinguish observed evidence from interpretation;
190
- 4. report uncertainty and disagreement;
191
- 5. state missing or not-applicable evidence;
192
- 6. explain context and limitations; and
193
- 7. offer non-prescriptive improvement options.
194
-
195
- Do not label a person, declare a work “top-tier,” predict success, recommend a
196
- decision, or conceal uncertainty behind a decimal.