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.
- package/CHANGELOG.md +26 -0
- package/LICENSE +201 -0
- package/README.md +138 -0
- package/README.zh-CN.md +138 -0
- package/bin/clearai.mjs +224 -0
- package/brand/README.md +41 -0
- package/brand/logo-512-dark.png +0 -0
- package/brand/logo-512.png +0 -0
- package/brand/logo-lockup-dark.png +0 -0
- package/brand/logo-lockup.png +0 -0
- package/brand/logo-lockup.svg +12 -0
- package/brand/logo-wordmark.svg +6 -0
- package/brand/logo.svg +19 -0
- package/cordis.patch.yml +39 -0
- package/lib/client.js +3071 -0
- package/lib/fold.js +1576 -0
- package/lib/host.js +605 -0
- package/package.json +65 -0
- package/presets/clearai/agent.cordis.yml +226 -0
- package/presets/clearai/plugins/brain.js +547 -0
- package/presets/clearai/plugins/clearai-kernel.js +5485 -0
- package/presets/clearai/plugins/ontology.js +306 -0
- package/presets/clearai/plugins/prompts.js +312 -0
- package/presets/clearai/preset.yml +5 -0
- package/presets/clearai/skills/clearai-loop/SKILL.md +89 -0
- package/presets/clearai/template/knowledge/README.md +25 -0
- package/presets/clearai/template/memory/README.md +34 -0
- package/presets/clearai/template/project.md +49 -0
- package/presets/clearai/template/skills/README.md +37 -0
- package/presets/clearai/template/skills/chart-diagram-qa/SKILL.md +43 -0
- package/presets/clearai/template/skills/citation-management/SKILL.md +73 -0
- package/presets/clearai/template/skills/citation-management/references/bibtex_formatting.md +908 -0
- package/presets/clearai/template/skills/citation-management/references/citation_validation.md +794 -0
- package/presets/clearai/template/skills/citation-management/references/google_scholar_search.md +725 -0
- package/presets/clearai/template/skills/citation-management/references/metadata_extraction.md +870 -0
- package/presets/clearai/template/skills/citation-management/references/pubmed_search.md +839 -0
- package/presets/clearai/template/skills/citation-management/scripts/doi_to_bibtex.py +204 -0
- package/presets/clearai/template/skills/citation-management/scripts/extract_metadata.py +569 -0
- package/presets/clearai/template/skills/citation-management/scripts/format_bibtex.py +349 -0
- package/presets/clearai/template/skills/citation-management/scripts/generate_schematic.py +139 -0
- package/presets/clearai/template/skills/citation-management/scripts/generate_schematic_ai.py +817 -0
- package/presets/clearai/template/skills/citation-management/scripts/search_google_scholar.py +282 -0
- package/presets/clearai/template/skills/citation-management/scripts/search_pubmed.py +398 -0
- package/presets/clearai/template/skills/citation-management/scripts/validate_citations.py +497 -0
- package/presets/clearai/template/skills/data-analysis/SKILL.md +92 -0
- package/presets/clearai/template/skills/data-analysis/checklists/readiness_check.md +23 -0
- package/presets/clearai/template/skills/data-analysis/templates/analysis_report.md.tpl +63 -0
- package/presets/clearai/template/skills/data-analysis/templates/cleaning_rules_draft.yaml.tpl +32 -0
- package/presets/clearai/template/skills/data-analysis/templates/data_dictionary.md.tpl +12 -0
- package/presets/clearai/template/skills/data-analysis/templates/domain_knowledge_template.md.tpl +316 -0
- package/presets/clearai/template/skills/data-analysis/templates/feature_candidates.json.tpl +20 -0
- package/presets/clearai/template/skills/data-analysis/templates/quality_scorecard.md.tpl +30 -0
- package/presets/clearai/template/skills/data-analysis/workflows/01-data-profiling.md +42 -0
- package/presets/clearai/template/skills/data-analysis/workflows/02-quality-audit.md +36 -0
- package/presets/clearai/template/skills/data-analysis/workflows/03-physical-correlation.md +25 -0
- package/presets/clearai/template/skills/data-analysis/workflows/04-unstructured-mining.md +26 -0
- package/presets/clearai/template/skills/data-qa-analysis/SKILL.md +102 -0
- package/presets/clearai/template/skills/data-qa-analysis/checklists/readiness_check.md +62 -0
- package/presets/clearai/template/skills/data-qa-analysis/templates/best_in_class_report.md.tpl +56 -0
- package/presets/clearai/template/skills/data-qa-analysis/templates/cleaning_rules_draft.yaml.tpl +56 -0
- package/presets/clearai/template/skills/data-qa-analysis/templates/data_dictionary.md.tpl +13 -0
- package/presets/clearai/template/skills/data-qa-analysis/templates/data_source_inventory_and_lineage.md.tpl +146 -0
- package/presets/clearai/template/skills/data-qa-analysis/templates/data_status_report.md.tpl +60 -0
- package/presets/clearai/template/skills/data-qa-analysis/templates/steady_state_rules.yaml.tpl +41 -0
- package/presets/clearai/template/skills/data-qa-analysis/templates/subsystem_registry.md.tpl +101 -0
- package/presets/clearai/template/skills/data-qa-analysis/templates/unified_execution_plan.md.tpl +100 -0
- package/presets/clearai/template/skills/data-qa-analysis/workflows/01-data-source-inventory-and-lineage.md +194 -0
- package/presets/clearai/template/skills/data-qa-analysis/workflows/02-data-alignment-and-tag-semantics.md +122 -0
- package/presets/clearai/template/skills/data-qa-analysis/workflows/03-steady-state-identification.md +126 -0
- package/presets/clearai/template/skills/data-qa-analysis/workflows/04-consumption-analysis.md +152 -0
- package/presets/clearai/template/skills/data-qa-analysis/workflows/05-best-in-class-and-optimization-space.md +78 -0
- package/presets/clearai/template/skills/domain-presearch/SKILL.md +131 -0
- package/presets/clearai/template/skills/domain-presearch/checklists/domain_checklist.md +24 -0
- package/presets/clearai/template/skills/domain-presearch/references/figure_code.md +78 -0
- package/presets/clearai/template/skills/domain-presearch/references/strategic_frameworks.md +38 -0
- package/presets/clearai/template/skills/exploration-loop/SKILL.md +81 -0
- package/presets/clearai/template/skills/exploratory-data-analysis/SKILL.md +77 -0
- package/presets/clearai/template/skills/exploratory-data-analysis/references/bioinformatics_genomics_formats.md +664 -0
- package/presets/clearai/template/skills/exploratory-data-analysis/references/chemistry_molecular_formats.md +664 -0
- package/presets/clearai/template/skills/exploratory-data-analysis/references/general_scientific_formats.md +518 -0
- package/presets/clearai/template/skills/exploratory-data-analysis/references/microscopy_imaging_formats.md +620 -0
- package/presets/clearai/template/skills/exploratory-data-analysis/references/proteomics_metabolomics_formats.md +517 -0
- package/presets/clearai/template/skills/exploratory-data-analysis/references/spectroscopy_analytical_formats.md +633 -0
- package/presets/clearai/template/skills/exploratory-data-analysis/scripts/eda_analyzer.py +547 -0
- package/presets/clearai/template/skills/hypothesis-generation/SKILL.md +73 -0
- package/presets/clearai/template/skills/hypothesis-generation/references/experimental_design_patterns.md +329 -0
- package/presets/clearai/template/skills/hypothesis-generation/references/hypothesis_quality_criteria.md +198 -0
- package/presets/clearai/template/skills/hypothesis-generation/references/literature_search_strategies.md +622 -0
- package/presets/clearai/template/skills/hypothesis-generation/scripts/generate_schematic.py +139 -0
- package/presets/clearai/template/skills/hypothesis-generation/scripts/generate_schematic_ai.py +817 -0
- package/presets/clearai/template/skills/literature-review/SKILL.md +72 -0
- package/presets/clearai/template/skills/literature-review/references/citation_styles.md +166 -0
- package/presets/clearai/template/skills/literature-review/references/database_strategies.md +455 -0
- package/presets/clearai/template/skills/literature-review/scripts/generate_pdf.py +176 -0
- package/presets/clearai/template/skills/literature-review/scripts/generate_schematic.py +139 -0
- package/presets/clearai/template/skills/literature-review/scripts/generate_schematic_ai.py +817 -0
- package/presets/clearai/template/skills/literature-review/scripts/search_databases.py +303 -0
- package/presets/clearai/template/skills/literature-review/scripts/verify_citations.py +221 -0
- package/presets/clearai/template/skills/paper-lookup/SKILL.md +59 -0
- package/presets/clearai/template/skills/paper-lookup/references/arxiv.md +161 -0
- package/presets/clearai/template/skills/paper-lookup/references/biorxiv.md +118 -0
- package/presets/clearai/template/skills/paper-lookup/references/core.md +150 -0
- package/presets/clearai/template/skills/paper-lookup/references/crossref.md +181 -0
- package/presets/clearai/template/skills/paper-lookup/references/medrxiv.md +104 -0
- package/presets/clearai/template/skills/paper-lookup/references/openalex.md +174 -0
- package/presets/clearai/template/skills/paper-lookup/references/pmc.md +152 -0
- package/presets/clearai/template/skills/paper-lookup/references/pubmed.md +124 -0
- package/presets/clearai/template/skills/paper-lookup/references/semantic-scholar.md +203 -0
- package/presets/clearai/template/skills/paper-lookup/references/unpaywall.md +127 -0
- package/presets/clearai/template/skills/process-presearch/SKILL.md +196 -0
- package/presets/clearai/template/skills/process-presearch/checklists/process_checklist.md +18 -0
- package/presets/clearai/template/skills/process-presearch/references/figure_code.md +107 -0
- package/presets/clearai/template/skills/process-presearch/references/source_attribution_example.md +22 -0
- package/presets/clearai/template/skills/process-understanding-extraction/SKILL.md +69 -0
- package/presets/clearai/template/skills/process-understanding-extraction/checklists/readiness_check.md +34 -0
- package/presets/clearai/template/skills/process-understanding-extraction/templates/docx_raw_dump_extractor.py.tpl +132 -0
- package/presets/clearai/template/skills/process-understanding-extraction/templates/entity_map_unit_topology.json.tpl +86 -0
- package/presets/clearai/template/skills/process-understanding-extraction/templates/process_brief.md.tpl +89 -0
- package/presets/clearai/template/skills/process-understanding-extraction/templates/process_brief_builder_from_raw_dump.py.tpl +203 -0
- package/presets/clearai/template/skills/process-understanding-extraction/templates/process_flow_mermaid.md.tpl +41 -0
- package/presets/clearai/template/skills/process-understanding-extraction/templates/unified_execution_plan.md.tpl +53 -0
- package/presets/clearai/template/skills/process-understanding-extraction/workflows/01-process-doc-discovery.md +173 -0
- package/presets/clearai/template/skills/process-understanding-extraction/workflows/02-process-understanding-and-diagramming.md +106 -0
- package/presets/clearai/template/skills/scientific-brainstorming/SKILL.md +64 -0
- package/presets/clearai/template/skills/scientific-brainstorming/references/brainstorming_methods.md +326 -0
- package/presets/clearai/template/skills/scientific-critical-thinking/SKILL.md +72 -0
- package/presets/clearai/template/skills/scientific-critical-thinking/references/common_biases.md +364 -0
- package/presets/clearai/template/skills/scientific-critical-thinking/references/evidence_hierarchy.md +485 -0
- package/presets/clearai/template/skills/scientific-critical-thinking/references/experimental_design.md +496 -0
- package/presets/clearai/template/skills/scientific-critical-thinking/references/logical_fallacies.md +478 -0
- package/presets/clearai/template/skills/scientific-critical-thinking/references/scientific_method.md +169 -0
- package/presets/clearai/template/skills/scientific-critical-thinking/references/statistical_pitfalls.md +506 -0
- package/presets/clearai/template/skills/skill-creator/SKILL.md +109 -0
- package/presets/clearai/template/skills/skill-creator/references/authoring-guide.md +89 -0
- package/presets/clearai/template/skills/statistical-analysis/SKILL.md +79 -0
- package/presets/clearai/template/skills/statistical-analysis/references/assumptions_and_diagnostics.md +369 -0
- package/presets/clearai/template/skills/statistical-analysis/references/bayesian_statistics.md +653 -0
- package/presets/clearai/template/skills/statistical-analysis/references/effect_sizes_and_power.md +578 -0
- package/presets/clearai/template/skills/statistical-analysis/references/reporting_standards.md +469 -0
- package/presets/clearai/template/skills/statistical-analysis/references/test_selection_guide.md +129 -0
- package/presets/clearai/template/skills/statistical-analysis/scripts/assumption_checks.py +538 -0
- package/presets/clearai/template/skills/web-artifact/SKILL.md +165 -0
- package/presets/clearai/template/skills/web-artifact/assets/renderer/renderer.css +229 -0
- package/presets/clearai/template/skills/web-artifact/assets/renderer/renderer.js +373 -0
- package/presets/clearai/template/skills/web-artifact/assets/vendor/elkjs/LICENSE +263 -0
- package/presets/clearai/template/skills/web-artifact/assets/vendor/elkjs/UPSTREAM.md +26 -0
- package/presets/clearai/template/skills/web-artifact/assets/vendor/elkjs/elk.bundled.js +6605 -0
- package/presets/clearai/template/skills/web-artifact/references/when-drawing-a-topology.md +150 -0
- package/presets/clearai/template/skills/web-artifact/references/when-the-page-must-work-offline.md +62 -0
- package/presets/clearai/template/skills/web-artifact/scripts/check_artifact.py +167 -0
- package/presets/clearai/template/skills/web-artifact/scripts/render_topology.js +272 -0
- package/presets/clearai/template/skills/what-if-oracle/LICENSE.txt +5 -0
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- package/presets/clearai/template/skills/what-if-oracle/references/scenario-templates.md +154 -0
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---
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name: citation-management
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description: |
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【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)。
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license: MIT license
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metadata:
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version: 1.0-clearai
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skill-author: K-Dense Inc. (adapted for ClearAI)
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tier: system
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origin: template
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created_at: '2026-06-12T02:47:05.406842+00:00'
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---
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# 引用管理 Skill(ClearAI 版)
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## 使用边界
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- **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。
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- **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)。
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## ClearAI 工具与路径映射
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- 元数据获取 → `bash`(CrossRef/PubMed API,见 `scripts/` 若已复制)
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- BibTeX 库 → `lab/knowledge/references.bib`
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- 校验报告 → `lab/knowledge/citation_audit.md`
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- 正式报告引用 → `products/reports/*.md` 文末 `[N]` + bib 键对应
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- 经验回写 → `clear/memory/citation_management_lessons.md`
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## 工作流
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### 1. 收集待引用项
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从 `literature-review`、`domain-presearch` 草稿提取 DOI/标题/URL。
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### 2. 元数据解析
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- DOI → CrossRef(`curl https://api.crossref.org/works/{doi}`)
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- PMID → PubMed E-utilities
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### 3. 生成 BibTeX
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```bibtex
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@article{key2024,
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title = {...},
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author = {...},
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journal = {...},
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year = {2024},
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}
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```
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写入 `lab/knowledge/references.bib`,键名规范:`AuthorYearKeyword`。
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### 4. 校验
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### 5. 与报告对齐
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- Markdown 正文 `[N]` 与 bib 键一一映射
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## 常用 bash 片段
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```bash
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# CrossRef DOI lookup
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curl -s "https://api.crossref.org/works/10.XXXX/yyyy" | python -m json.tool
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```
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更多脚本见已复制 `scripts/` 目录(按需调整输出路径到 `lab/knowledge/`)。
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