clearai-dsh 0.3.0 → 0.4.0

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Files changed (148) hide show
  1. package/CHANGELOG.md +147 -0
  2. package/README.md +28 -28
  3. package/README.zh-CN.md +28 -28
  4. package/lib/client.js +861 -2555
  5. package/lib/domain-language.js +552 -48
  6. package/lib/fold.js +351 -1015
  7. package/lib/host.js +47 -557
  8. package/lib/invariant.js +9 -12
  9. package/lib/knowledge-view.js +363 -226
  10. package/lib/lang.js +81 -0
  11. package/package.json +1 -1
  12. package/presets/clearai/agent.cordis.yml +54 -82
  13. package/presets/clearai/clearai.patch.yml +54 -82
  14. package/presets/clearai/plugins/clearai-kernel.js +1590 -5437
  15. package/presets/clearai/plugins/ontology.js +56 -14
  16. package/presets/clearai/plugins/prompts.js +73 -363
  17. package/presets/clearai/skills/clearai-loop/SKILL.md +73 -59
  18. package/presets/clearai/plugins/brain.js +0 -547
  19. package/presets/clearai/plugins/commands.js +0 -199
  20. package/presets/clearai/template/knowledge/README.md +0 -25
  21. package/presets/clearai/template/memory/README.md +0 -34
  22. package/presets/clearai/template/project.md +0 -49
  23. package/presets/clearai/template/skills/README.md +0 -37
  24. package/presets/clearai/template/skills/chart-diagram-qa/SKILL.md +0 -43
  25. package/presets/clearai/template/skills/citation-management/SKILL.md +0 -73
  26. package/presets/clearai/template/skills/citation-management/references/bibtex_formatting.md +0 -908
  27. package/presets/clearai/template/skills/citation-management/references/citation_validation.md +0 -794
  28. package/presets/clearai/template/skills/citation-management/references/google_scholar_search.md +0 -725
  29. package/presets/clearai/template/skills/citation-management/references/metadata_extraction.md +0 -870
  30. package/presets/clearai/template/skills/citation-management/references/pubmed_search.md +0 -839
  31. package/presets/clearai/template/skills/citation-management/scripts/doi_to_bibtex.py +0 -204
  32. package/presets/clearai/template/skills/citation-management/scripts/extract_metadata.py +0 -569
  33. package/presets/clearai/template/skills/citation-management/scripts/format_bibtex.py +0 -349
  34. package/presets/clearai/template/skills/citation-management/scripts/generate_schematic.py +0 -139
  35. package/presets/clearai/template/skills/citation-management/scripts/generate_schematic_ai.py +0 -817
  36. package/presets/clearai/template/skills/citation-management/scripts/search_google_scholar.py +0 -282
  37. package/presets/clearai/template/skills/citation-management/scripts/search_pubmed.py +0 -398
  38. package/presets/clearai/template/skills/citation-management/scripts/validate_citations.py +0 -497
  39. package/presets/clearai/template/skills/data-analysis/SKILL.md +0 -92
  40. package/presets/clearai/template/skills/data-analysis/checklists/readiness_check.md +0 -23
  41. package/presets/clearai/template/skills/data-analysis/templates/analysis_report.md.tpl +0 -63
  42. package/presets/clearai/template/skills/data-analysis/templates/cleaning_rules_draft.yaml.tpl +0 -32
  43. package/presets/clearai/template/skills/data-analysis/templates/data_dictionary.md.tpl +0 -12
  44. package/presets/clearai/template/skills/data-analysis/templates/domain_knowledge_template.md.tpl +0 -316
  45. package/presets/clearai/template/skills/data-analysis/templates/feature_candidates.json.tpl +0 -20
  46. package/presets/clearai/template/skills/data-analysis/templates/quality_scorecard.md.tpl +0 -30
  47. package/presets/clearai/template/skills/data-analysis/workflows/01-data-profiling.md +0 -42
  48. package/presets/clearai/template/skills/data-analysis/workflows/02-quality-audit.md +0 -36
  49. package/presets/clearai/template/skills/data-analysis/workflows/03-physical-correlation.md +0 -25
  50. package/presets/clearai/template/skills/data-analysis/workflows/04-unstructured-mining.md +0 -26
  51. package/presets/clearai/template/skills/data-qa-analysis/SKILL.md +0 -102
  52. package/presets/clearai/template/skills/data-qa-analysis/checklists/readiness_check.md +0 -62
  53. package/presets/clearai/template/skills/data-qa-analysis/templates/best_in_class_report.md.tpl +0 -56
  54. package/presets/clearai/template/skills/data-qa-analysis/templates/cleaning_rules_draft.yaml.tpl +0 -56
  55. package/presets/clearai/template/skills/data-qa-analysis/templates/data_dictionary.md.tpl +0 -13
  56. package/presets/clearai/template/skills/data-qa-analysis/templates/data_source_inventory_and_lineage.md.tpl +0 -146
  57. package/presets/clearai/template/skills/data-qa-analysis/templates/data_status_report.md.tpl +0 -60
  58. package/presets/clearai/template/skills/data-qa-analysis/templates/steady_state_rules.yaml.tpl +0 -41
  59. package/presets/clearai/template/skills/data-qa-analysis/templates/subsystem_registry.md.tpl +0 -101
  60. package/presets/clearai/template/skills/data-qa-analysis/templates/unified_execution_plan.md.tpl +0 -100
  61. package/presets/clearai/template/skills/data-qa-analysis/workflows/01-data-source-inventory-and-lineage.md +0 -194
  62. package/presets/clearai/template/skills/data-qa-analysis/workflows/02-data-alignment-and-tag-semantics.md +0 -122
  63. package/presets/clearai/template/skills/data-qa-analysis/workflows/03-steady-state-identification.md +0 -126
  64. package/presets/clearai/template/skills/data-qa-analysis/workflows/04-consumption-analysis.md +0 -152
  65. package/presets/clearai/template/skills/data-qa-analysis/workflows/05-best-in-class-and-optimization-space.md +0 -78
  66. package/presets/clearai/template/skills/domain-presearch/SKILL.md +0 -131
  67. package/presets/clearai/template/skills/domain-presearch/checklists/domain_checklist.md +0 -24
  68. package/presets/clearai/template/skills/domain-presearch/references/figure_code.md +0 -78
  69. package/presets/clearai/template/skills/domain-presearch/references/strategic_frameworks.md +0 -38
  70. package/presets/clearai/template/skills/exploration-loop/SKILL.md +0 -81
  71. package/presets/clearai/template/skills/exploratory-data-analysis/SKILL.md +0 -77
  72. package/presets/clearai/template/skills/exploratory-data-analysis/references/bioinformatics_genomics_formats.md +0 -664
  73. package/presets/clearai/template/skills/exploratory-data-analysis/references/chemistry_molecular_formats.md +0 -664
  74. package/presets/clearai/template/skills/exploratory-data-analysis/references/general_scientific_formats.md +0 -518
  75. package/presets/clearai/template/skills/exploratory-data-analysis/references/microscopy_imaging_formats.md +0 -620
  76. package/presets/clearai/template/skills/exploratory-data-analysis/references/proteomics_metabolomics_formats.md +0 -517
  77. package/presets/clearai/template/skills/exploratory-data-analysis/references/spectroscopy_analytical_formats.md +0 -633
  78. package/presets/clearai/template/skills/exploratory-data-analysis/scripts/eda_analyzer.py +0 -547
  79. package/presets/clearai/template/skills/hypothesis-generation/SKILL.md +0 -73
  80. package/presets/clearai/template/skills/hypothesis-generation/references/experimental_design_patterns.md +0 -329
  81. package/presets/clearai/template/skills/hypothesis-generation/references/hypothesis_quality_criteria.md +0 -198
  82. package/presets/clearai/template/skills/hypothesis-generation/references/literature_search_strategies.md +0 -622
  83. package/presets/clearai/template/skills/hypothesis-generation/scripts/generate_schematic.py +0 -139
  84. package/presets/clearai/template/skills/hypothesis-generation/scripts/generate_schematic_ai.py +0 -817
  85. package/presets/clearai/template/skills/literature-review/SKILL.md +0 -72
  86. package/presets/clearai/template/skills/literature-review/references/citation_styles.md +0 -166
  87. package/presets/clearai/template/skills/literature-review/references/database_strategies.md +0 -455
  88. package/presets/clearai/template/skills/literature-review/scripts/generate_pdf.py +0 -176
  89. package/presets/clearai/template/skills/literature-review/scripts/generate_schematic.py +0 -139
  90. package/presets/clearai/template/skills/literature-review/scripts/generate_schematic_ai.py +0 -817
  91. package/presets/clearai/template/skills/literature-review/scripts/search_databases.py +0 -303
  92. package/presets/clearai/template/skills/literature-review/scripts/verify_citations.py +0 -221
  93. package/presets/clearai/template/skills/paper-lookup/SKILL.md +0 -59
  94. package/presets/clearai/template/skills/paper-lookup/references/arxiv.md +0 -161
  95. package/presets/clearai/template/skills/paper-lookup/references/biorxiv.md +0 -118
  96. package/presets/clearai/template/skills/paper-lookup/references/core.md +0 -150
  97. package/presets/clearai/template/skills/paper-lookup/references/crossref.md +0 -181
  98. package/presets/clearai/template/skills/paper-lookup/references/medrxiv.md +0 -104
  99. package/presets/clearai/template/skills/paper-lookup/references/openalex.md +0 -174
  100. package/presets/clearai/template/skills/paper-lookup/references/pmc.md +0 -152
  101. package/presets/clearai/template/skills/paper-lookup/references/pubmed.md +0 -124
  102. package/presets/clearai/template/skills/paper-lookup/references/semantic-scholar.md +0 -203
  103. package/presets/clearai/template/skills/paper-lookup/references/unpaywall.md +0 -127
  104. package/presets/clearai/template/skills/process-presearch/SKILL.md +0 -196
  105. package/presets/clearai/template/skills/process-presearch/checklists/process_checklist.md +0 -18
  106. package/presets/clearai/template/skills/process-presearch/references/figure_code.md +0 -107
  107. package/presets/clearai/template/skills/process-presearch/references/source_attribution_example.md +0 -22
  108. package/presets/clearai/template/skills/process-understanding-extraction/SKILL.md +0 -69
  109. package/presets/clearai/template/skills/process-understanding-extraction/checklists/readiness_check.md +0 -34
  110. package/presets/clearai/template/skills/process-understanding-extraction/templates/docx_raw_dump_extractor.py.tpl +0 -132
  111. package/presets/clearai/template/skills/process-understanding-extraction/templates/entity_map_unit_topology.json.tpl +0 -86
  112. package/presets/clearai/template/skills/process-understanding-extraction/templates/process_brief.md.tpl +0 -89
  113. package/presets/clearai/template/skills/process-understanding-extraction/templates/process_brief_builder_from_raw_dump.py.tpl +0 -203
  114. package/presets/clearai/template/skills/process-understanding-extraction/templates/process_flow_mermaid.md.tpl +0 -41
  115. package/presets/clearai/template/skills/process-understanding-extraction/templates/unified_execution_plan.md.tpl +0 -53
  116. package/presets/clearai/template/skills/process-understanding-extraction/workflows/01-process-doc-discovery.md +0 -173
  117. package/presets/clearai/template/skills/process-understanding-extraction/workflows/02-process-understanding-and-diagramming.md +0 -106
  118. package/presets/clearai/template/skills/scientific-brainstorming/SKILL.md +0 -64
  119. package/presets/clearai/template/skills/scientific-brainstorming/references/brainstorming_methods.md +0 -326
  120. package/presets/clearai/template/skills/scientific-critical-thinking/SKILL.md +0 -72
  121. package/presets/clearai/template/skills/scientific-critical-thinking/references/common_biases.md +0 -364
  122. package/presets/clearai/template/skills/scientific-critical-thinking/references/evidence_hierarchy.md +0 -485
  123. package/presets/clearai/template/skills/scientific-critical-thinking/references/experimental_design.md +0 -496
  124. package/presets/clearai/template/skills/scientific-critical-thinking/references/logical_fallacies.md +0 -478
  125. package/presets/clearai/template/skills/scientific-critical-thinking/references/scientific_method.md +0 -169
  126. package/presets/clearai/template/skills/scientific-critical-thinking/references/statistical_pitfalls.md +0 -506
  127. package/presets/clearai/template/skills/skill-creator/SKILL.md +0 -109
  128. package/presets/clearai/template/skills/skill-creator/references/authoring-guide.md +0 -89
  129. package/presets/clearai/template/skills/statistical-analysis/SKILL.md +0 -79
  130. package/presets/clearai/template/skills/statistical-analysis/references/assumptions_and_diagnostics.md +0 -369
  131. package/presets/clearai/template/skills/statistical-analysis/references/bayesian_statistics.md +0 -653
  132. package/presets/clearai/template/skills/statistical-analysis/references/effect_sizes_and_power.md +0 -578
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  135. package/presets/clearai/template/skills/statistical-analysis/scripts/assumption_checks.py +0 -538
  136. package/presets/clearai/template/skills/web-artifact/SKILL.md +0 -165
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  139. package/presets/clearai/template/skills/web-artifact/assets/vendor/elkjs/LICENSE +0 -263
  140. package/presets/clearai/template/skills/web-artifact/assets/vendor/elkjs/UPSTREAM.md +0 -26
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  145. package/presets/clearai/template/skills/web-artifact/scripts/render_topology.js +0 -272
  146. package/presets/clearai/template/skills/what-if-oracle/LICENSE.txt +0 -5
  147. package/presets/clearai/template/skills/what-if-oracle/SKILL.md +0 -72
  148. package/presets/clearai/template/skills/what-if-oracle/references/scenario-templates.md +0 -154

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