clearai-dsh 0.1.0

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 (154) hide show
  1. package/CHANGELOG.md +26 -0
  2. package/LICENSE +201 -0
  3. package/README.md +138 -0
  4. package/README.zh-CN.md +138 -0
  5. package/bin/clearai.mjs +224 -0
  6. package/brand/README.md +41 -0
  7. package/brand/logo-512-dark.png +0 -0
  8. package/brand/logo-512.png +0 -0
  9. package/brand/logo-lockup-dark.png +0 -0
  10. package/brand/logo-lockup.png +0 -0
  11. package/brand/logo-lockup.svg +12 -0
  12. package/brand/logo-wordmark.svg +6 -0
  13. package/brand/logo.svg +19 -0
  14. package/cordis.patch.yml +39 -0
  15. package/lib/client.js +3071 -0
  16. package/lib/fold.js +1576 -0
  17. package/lib/host.js +605 -0
  18. package/package.json +65 -0
  19. package/presets/clearai/agent.cordis.yml +226 -0
  20. package/presets/clearai/plugins/brain.js +547 -0
  21. package/presets/clearai/plugins/clearai-kernel.js +5485 -0
  22. package/presets/clearai/plugins/ontology.js +306 -0
  23. package/presets/clearai/plugins/prompts.js +312 -0
  24. package/presets/clearai/preset.yml +5 -0
  25. package/presets/clearai/skills/clearai-loop/SKILL.md +89 -0
  26. package/presets/clearai/template/knowledge/README.md +25 -0
  27. package/presets/clearai/template/memory/README.md +34 -0
  28. package/presets/clearai/template/project.md +49 -0
  29. package/presets/clearai/template/skills/README.md +37 -0
  30. package/presets/clearai/template/skills/chart-diagram-qa/SKILL.md +43 -0
  31. package/presets/clearai/template/skills/citation-management/SKILL.md +73 -0
  32. package/presets/clearai/template/skills/citation-management/references/bibtex_formatting.md +908 -0
  33. package/presets/clearai/template/skills/citation-management/references/citation_validation.md +794 -0
  34. package/presets/clearai/template/skills/citation-management/references/google_scholar_search.md +725 -0
  35. package/presets/clearai/template/skills/citation-management/references/metadata_extraction.md +870 -0
  36. package/presets/clearai/template/skills/citation-management/references/pubmed_search.md +839 -0
  37. package/presets/clearai/template/skills/citation-management/scripts/doi_to_bibtex.py +204 -0
  38. package/presets/clearai/template/skills/citation-management/scripts/extract_metadata.py +569 -0
  39. package/presets/clearai/template/skills/citation-management/scripts/format_bibtex.py +349 -0
  40. package/presets/clearai/template/skills/citation-management/scripts/generate_schematic.py +139 -0
  41. package/presets/clearai/template/skills/citation-management/scripts/generate_schematic_ai.py +817 -0
  42. package/presets/clearai/template/skills/citation-management/scripts/search_google_scholar.py +282 -0
  43. package/presets/clearai/template/skills/citation-management/scripts/search_pubmed.py +398 -0
  44. package/presets/clearai/template/skills/citation-management/scripts/validate_citations.py +497 -0
  45. package/presets/clearai/template/skills/data-analysis/SKILL.md +92 -0
  46. package/presets/clearai/template/skills/data-analysis/checklists/readiness_check.md +23 -0
  47. package/presets/clearai/template/skills/data-analysis/templates/analysis_report.md.tpl +63 -0
  48. package/presets/clearai/template/skills/data-analysis/templates/cleaning_rules_draft.yaml.tpl +32 -0
  49. package/presets/clearai/template/skills/data-analysis/templates/data_dictionary.md.tpl +12 -0
  50. package/presets/clearai/template/skills/data-analysis/templates/domain_knowledge_template.md.tpl +316 -0
  51. package/presets/clearai/template/skills/data-analysis/templates/feature_candidates.json.tpl +20 -0
  52. package/presets/clearai/template/skills/data-analysis/templates/quality_scorecard.md.tpl +30 -0
  53. package/presets/clearai/template/skills/data-analysis/workflows/01-data-profiling.md +42 -0
  54. package/presets/clearai/template/skills/data-analysis/workflows/02-quality-audit.md +36 -0
  55. package/presets/clearai/template/skills/data-analysis/workflows/03-physical-correlation.md +25 -0
  56. package/presets/clearai/template/skills/data-analysis/workflows/04-unstructured-mining.md +26 -0
  57. package/presets/clearai/template/skills/data-qa-analysis/SKILL.md +102 -0
  58. package/presets/clearai/template/skills/data-qa-analysis/checklists/readiness_check.md +62 -0
  59. package/presets/clearai/template/skills/data-qa-analysis/templates/best_in_class_report.md.tpl +56 -0
  60. package/presets/clearai/template/skills/data-qa-analysis/templates/cleaning_rules_draft.yaml.tpl +56 -0
  61. package/presets/clearai/template/skills/data-qa-analysis/templates/data_dictionary.md.tpl +13 -0
  62. package/presets/clearai/template/skills/data-qa-analysis/templates/data_source_inventory_and_lineage.md.tpl +146 -0
  63. package/presets/clearai/template/skills/data-qa-analysis/templates/data_status_report.md.tpl +60 -0
  64. package/presets/clearai/template/skills/data-qa-analysis/templates/steady_state_rules.yaml.tpl +41 -0
  65. package/presets/clearai/template/skills/data-qa-analysis/templates/subsystem_registry.md.tpl +101 -0
  66. package/presets/clearai/template/skills/data-qa-analysis/templates/unified_execution_plan.md.tpl +100 -0
  67. package/presets/clearai/template/skills/data-qa-analysis/workflows/01-data-source-inventory-and-lineage.md +194 -0
  68. package/presets/clearai/template/skills/data-qa-analysis/workflows/02-data-alignment-and-tag-semantics.md +122 -0
  69. package/presets/clearai/template/skills/data-qa-analysis/workflows/03-steady-state-identification.md +126 -0
  70. package/presets/clearai/template/skills/data-qa-analysis/workflows/04-consumption-analysis.md +152 -0
  71. package/presets/clearai/template/skills/data-qa-analysis/workflows/05-best-in-class-and-optimization-space.md +78 -0
  72. package/presets/clearai/template/skills/domain-presearch/SKILL.md +131 -0
  73. package/presets/clearai/template/skills/domain-presearch/checklists/domain_checklist.md +24 -0
  74. package/presets/clearai/template/skills/domain-presearch/references/figure_code.md +78 -0
  75. package/presets/clearai/template/skills/domain-presearch/references/strategic_frameworks.md +38 -0
  76. package/presets/clearai/template/skills/exploration-loop/SKILL.md +81 -0
  77. package/presets/clearai/template/skills/exploratory-data-analysis/SKILL.md +77 -0
  78. package/presets/clearai/template/skills/exploratory-data-analysis/references/bioinformatics_genomics_formats.md +664 -0
  79. package/presets/clearai/template/skills/exploratory-data-analysis/references/chemistry_molecular_formats.md +664 -0
  80. package/presets/clearai/template/skills/exploratory-data-analysis/references/general_scientific_formats.md +518 -0
  81. package/presets/clearai/template/skills/exploratory-data-analysis/references/microscopy_imaging_formats.md +620 -0
  82. package/presets/clearai/template/skills/exploratory-data-analysis/references/proteomics_metabolomics_formats.md +517 -0
  83. package/presets/clearai/template/skills/exploratory-data-analysis/references/spectroscopy_analytical_formats.md +633 -0
  84. package/presets/clearai/template/skills/exploratory-data-analysis/scripts/eda_analyzer.py +547 -0
  85. package/presets/clearai/template/skills/hypothesis-generation/SKILL.md +73 -0
  86. package/presets/clearai/template/skills/hypothesis-generation/references/experimental_design_patterns.md +329 -0
  87. package/presets/clearai/template/skills/hypothesis-generation/references/hypothesis_quality_criteria.md +198 -0
  88. package/presets/clearai/template/skills/hypothesis-generation/references/literature_search_strategies.md +622 -0
  89. package/presets/clearai/template/skills/hypothesis-generation/scripts/generate_schematic.py +139 -0
  90. package/presets/clearai/template/skills/hypothesis-generation/scripts/generate_schematic_ai.py +817 -0
  91. package/presets/clearai/template/skills/literature-review/SKILL.md +72 -0
  92. package/presets/clearai/template/skills/literature-review/references/citation_styles.md +166 -0
  93. package/presets/clearai/template/skills/literature-review/references/database_strategies.md +455 -0
  94. package/presets/clearai/template/skills/literature-review/scripts/generate_pdf.py +176 -0
  95. package/presets/clearai/template/skills/literature-review/scripts/generate_schematic.py +139 -0
  96. package/presets/clearai/template/skills/literature-review/scripts/generate_schematic_ai.py +817 -0
  97. package/presets/clearai/template/skills/literature-review/scripts/search_databases.py +303 -0
  98. package/presets/clearai/template/skills/literature-review/scripts/verify_citations.py +221 -0
  99. package/presets/clearai/template/skills/paper-lookup/SKILL.md +59 -0
  100. package/presets/clearai/template/skills/paper-lookup/references/arxiv.md +161 -0
  101. package/presets/clearai/template/skills/paper-lookup/references/biorxiv.md +118 -0
  102. package/presets/clearai/template/skills/paper-lookup/references/core.md +150 -0
  103. package/presets/clearai/template/skills/paper-lookup/references/crossref.md +181 -0
  104. package/presets/clearai/template/skills/paper-lookup/references/medrxiv.md +104 -0
  105. package/presets/clearai/template/skills/paper-lookup/references/openalex.md +174 -0
  106. package/presets/clearai/template/skills/paper-lookup/references/pmc.md +152 -0
  107. package/presets/clearai/template/skills/paper-lookup/references/pubmed.md +124 -0
  108. package/presets/clearai/template/skills/paper-lookup/references/semantic-scholar.md +203 -0
  109. package/presets/clearai/template/skills/paper-lookup/references/unpaywall.md +127 -0
  110. package/presets/clearai/template/skills/process-presearch/SKILL.md +196 -0
  111. package/presets/clearai/template/skills/process-presearch/checklists/process_checklist.md +18 -0
  112. package/presets/clearai/template/skills/process-presearch/references/figure_code.md +107 -0
  113. package/presets/clearai/template/skills/process-presearch/references/source_attribution_example.md +22 -0
  114. package/presets/clearai/template/skills/process-understanding-extraction/SKILL.md +69 -0
  115. package/presets/clearai/template/skills/process-understanding-extraction/checklists/readiness_check.md +34 -0
  116. package/presets/clearai/template/skills/process-understanding-extraction/templates/docx_raw_dump_extractor.py.tpl +132 -0
  117. package/presets/clearai/template/skills/process-understanding-extraction/templates/entity_map_unit_topology.json.tpl +86 -0
  118. package/presets/clearai/template/skills/process-understanding-extraction/templates/process_brief.md.tpl +89 -0
  119. package/presets/clearai/template/skills/process-understanding-extraction/templates/process_brief_builder_from_raw_dump.py.tpl +203 -0
  120. package/presets/clearai/template/skills/process-understanding-extraction/templates/process_flow_mermaid.md.tpl +41 -0
  121. package/presets/clearai/template/skills/process-understanding-extraction/templates/unified_execution_plan.md.tpl +53 -0
  122. package/presets/clearai/template/skills/process-understanding-extraction/workflows/01-process-doc-discovery.md +173 -0
  123. package/presets/clearai/template/skills/process-understanding-extraction/workflows/02-process-understanding-and-diagramming.md +106 -0
  124. package/presets/clearai/template/skills/scientific-brainstorming/SKILL.md +64 -0
  125. package/presets/clearai/template/skills/scientific-brainstorming/references/brainstorming_methods.md +326 -0
  126. package/presets/clearai/template/skills/scientific-critical-thinking/SKILL.md +72 -0
  127. package/presets/clearai/template/skills/scientific-critical-thinking/references/common_biases.md +364 -0
  128. package/presets/clearai/template/skills/scientific-critical-thinking/references/evidence_hierarchy.md +485 -0
  129. package/presets/clearai/template/skills/scientific-critical-thinking/references/experimental_design.md +496 -0
  130. package/presets/clearai/template/skills/scientific-critical-thinking/references/logical_fallacies.md +478 -0
  131. package/presets/clearai/template/skills/scientific-critical-thinking/references/scientific_method.md +169 -0
  132. package/presets/clearai/template/skills/scientific-critical-thinking/references/statistical_pitfalls.md +506 -0
  133. package/presets/clearai/template/skills/skill-creator/SKILL.md +109 -0
  134. package/presets/clearai/template/skills/skill-creator/references/authoring-guide.md +89 -0
  135. package/presets/clearai/template/skills/statistical-analysis/SKILL.md +79 -0
  136. package/presets/clearai/template/skills/statistical-analysis/references/assumptions_and_diagnostics.md +369 -0
  137. package/presets/clearai/template/skills/statistical-analysis/references/bayesian_statistics.md +653 -0
  138. package/presets/clearai/template/skills/statistical-analysis/references/effect_sizes_and_power.md +578 -0
  139. package/presets/clearai/template/skills/statistical-analysis/references/reporting_standards.md +469 -0
  140. package/presets/clearai/template/skills/statistical-analysis/references/test_selection_guide.md +129 -0
  141. package/presets/clearai/template/skills/statistical-analysis/scripts/assumption_checks.py +538 -0
  142. package/presets/clearai/template/skills/web-artifact/SKILL.md +165 -0
  143. package/presets/clearai/template/skills/web-artifact/assets/renderer/renderer.css +229 -0
  144. package/presets/clearai/template/skills/web-artifact/assets/renderer/renderer.js +373 -0
  145. package/presets/clearai/template/skills/web-artifact/assets/vendor/elkjs/LICENSE +263 -0
  146. package/presets/clearai/template/skills/web-artifact/assets/vendor/elkjs/UPSTREAM.md +26 -0
  147. package/presets/clearai/template/skills/web-artifact/assets/vendor/elkjs/elk.bundled.js +6605 -0
  148. package/presets/clearai/template/skills/web-artifact/references/when-drawing-a-topology.md +150 -0
  149. package/presets/clearai/template/skills/web-artifact/references/when-the-page-must-work-offline.md +62 -0
  150. package/presets/clearai/template/skills/web-artifact/scripts/check_artifact.py +167 -0
  151. package/presets/clearai/template/skills/web-artifact/scripts/render_topology.js +272 -0
  152. package/presets/clearai/template/skills/what-if-oracle/LICENSE.txt +5 -0
  153. package/presets/clearai/template/skills/what-if-oracle/SKILL.md +72 -0
  154. package/presets/clearai/template/skills/what-if-oracle/references/scenario-templates.md +154 -0
@@ -0,0 +1,73 @@
1
+ ---
2
+ name: citation-management
3
+ description: |
4
+ 【引用管理·BibTeX】检索论文元数据、DOI→BibTeX、校验与去重。适用:预研/综述报告文末引用统一、交付前引用准确性检查。不适用:全文综述撰写(用 literature-review);一般网页来源(用 web_search sources 标注)。
5
+ license: MIT license
6
+ metadata:
7
+ version: 1.0-clearai
8
+ skill-author: K-Dense Inc. (adapted for ClearAI)
9
+ tier: system
10
+ origin: template
11
+ created_at: '2026-06-12T02:47:05.406842+00:00'
12
+ ---
13
+
14
+ # 引用管理 Skill(ClearAI 版)
15
+
16
+ ## 使用边界
17
+
18
+ - **适用**:构建/清洗 `references.bib`;验证 DOI/PMID;报告交付前引用去重与格式统一。
19
+ - **不适用**:替代 `paper-lookup` 做大规模检索;非学术网页引用(用手动 `[N]` 列表)。
20
+
21
+ ## ClearAI 工具与路径映射
22
+
23
+ - 元数据获取 → `bash`(CrossRef/PubMed API,见 `scripts/` 若已复制)
24
+ - BibTeX 库 → `lab/knowledge/references.bib`
25
+ - 校验报告 → `lab/knowledge/citation_audit.md`
26
+ - 正式报告引用 → `products/reports/*.md` 文末 `[N]` + bib 键对应
27
+ - 经验回写 → `clear/memory/citation_management_lessons.md`
28
+
29
+ ## 工作流
30
+
31
+ ### 1. 收集待引用项
32
+
33
+ 从 `literature-review`、`domain-presearch` 草稿提取 DOI/标题/URL。
34
+
35
+ ### 2. 元数据解析
36
+
37
+ - DOI → CrossRef(`curl https://api.crossref.org/works/{doi}`)
38
+ - PMID → PubMed E-utilities
39
+ - 无 DOI:用 `paper-lookup` 或 `web_search` 补全
40
+
41
+ ### 3. 生成 BibTeX
42
+
43
+ ```bibtex
44
+ @article{key2024,
45
+ title = {...},
46
+ author = {...},
47
+ journal = {...},
48
+ year = {2024},
49
+ doi = {...}
50
+ }
51
+ ```
52
+
53
+ 写入 `lab/knowledge/references.bib`,键名规范:`AuthorYearKeyword`。
54
+
55
+ ### 4. 校验
56
+
57
+ - 作者/年份/期刊与原文一致
58
+ - 重复键合并
59
+ - 缺失 DOI 标注待补
60
+
61
+ ### 5. 与报告对齐
62
+
63
+ - Markdown 正文 `[N]` 与 bib 键一一映射
64
+ - 交付前输出 `lab/knowledge/citation_audit.md`:通过/待修/删除
65
+
66
+ ## 常用 bash 片段
67
+
68
+ ```bash
69
+ # CrossRef DOI lookup
70
+ curl -s "https://api.crossref.org/works/10.XXXX/yyyy" | python -m json.tool
71
+ ```
72
+
73
+ 更多脚本见已复制 `scripts/` 目录(按需调整输出路径到 `lab/knowledge/`)。