Add HED-Assistant with comprehensive documentation support#18
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Implements HED (Hierarchical Event Descriptors) assistant following BIDS assistant pattern. Provides guidance on HED annotation based on official specification and resources. Features: - 41 documentation sources across HED specification and resources - 4 preloaded core documents (Introduction, Terminology, Basic Annotation) - 37 on-demand docs organized by category (specification, tools, quickstart, core concepts, advanced topics, integration, reference) - Comprehensive system prompt with HED-specific guidance - Integration tests covering all components Files: - hedAssistantSystemPrompt.ts: System prompt for HED guidance - retrieveHedDocs.tsx: Documentation retrieval with 41 sources - getTools.ts: Tool registration - preferences.tsx: UI preferences and suggested prompts - integration.test.ts: 11 integration tests (all passing) Registered in App.tsx and tools/getTools.ts Updated README to include HED-Assistant as 8th assistant
Owner
|
@neuromechanist This is great! This is now deployed: |
Contributor
Author
|
cc @VisLab |
yarikoptic
reviewed
Nov 13, 2025
| "https://raw.githubusercontent.com/hed-standard/hed-specification/main/docs/source/08_HED_ontology.md", | ||
| includeFromStart: false, | ||
| category: "specification-details", | ||
| }, |
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here is what the script from
gives for the hed-specification
❯ ./doc_pages_index.py https://www.hedtags.org/hed-specification/
Detecting documentation type for https://www.hedtags.org/hed-specification/
✓ Detected: Sphinx documentation
Fetching Sphinx search index from: https://www.hedtags.org/hed-specification/searchindex.js
Found 11 documents
Checking for _sources/ directory...
✗ No _sources/ directory found
Consider providing --source-repo for source file URLs
{
"docs_url": "https://www.hedtags.org/hed-specification/",
"doc_type": "sphinx",
"has_sources_dir": false,
"total_pages": 11,
"pages": [
{
"docname": "01_Introduction",
"title": "1. Introduction to HED",
"html_url": "https://www.hedtags.org/hed-specification/01_Introduction.html",
"source_filename": "01_Introduction.rst"
},
{
"docname": "02_Terminology",
"title": "2. HED terminology",
"html_url": "https://www.hedtags.org/hed-specification/02_Terminology.html",
"source_filename": "02_Terminology.rst"
},
{
"docname": "03_HED_formats",
"title": "3. HED formats",
"html_url": "https://www.hedtags.org/hed-specification/03_HED_formats.html",
"source_filename": "03_HED_formats.rst"
},
{
"docname": "04_Basic_annotation",
"title": "4. Basic annotation",
"html_url": "https://www.hedtags.org/hed-specification/04_Basic_annotation.html",
"source_filename": "04_Basic_annotation.rst"
},
{
"docname": "05_Advanced_annotation",
"title": "5. Advanced annotation",
"html_url": "https://www.hedtags.org/hed-specification/05_Advanced_annotation.html",
"source_filename": "05_Advanced_annotation.rst"
},
{
"docname": "06_Infrastructure_and_tools",
"title": "6. Infrastructure and tools",
"html_url": "https://www.hedtags.org/hed-specification/06_Infrastructure_and_tools.html",
"source_filename": "06_Infrastructure_and_tools.rst"
},
{
"docname": "07_Library_schemas",
"title": "7. Library schemas",
"html_url": "https://www.hedtags.org/hed-specification/07_Library_schemas.html",
"source_filename": "07_Library_schemas.rst"
},
{
"docname": "08_HED_ontology",
"title": "8. The HED ontology",
"html_url": "https://www.hedtags.org/hed-specification/08_HED_ontology.html",
"source_filename": "08_HED_ontology.rst"
},
{
"docname": "Appendix_A",
"title": "A. Schema format details",
"html_url": "https://www.hedtags.org/hed-specification/Appendix_A.html",
"source_filename": "Appendix_A.rst"
},
{
"docname": "Appendix_B",
"title": "B. HED errors",
"html_url": "https://www.hedtags.org/hed-specification/Appendix_B.html",
"source_filename": "Appendix_B.rst"
},
{
"docname": "index",
"title": "HED Specification",
"html_url": "https://www.hedtags.org/hed-specification/index.html",
"source_filename": "index.rst"
}
]
}
and below for hed-resources
yarikoptic
reviewed
Nov 13, 2025
| title: "HED Annotation Quickstart", | ||
| url: "https://www.hedtags.org/hed-resources/HedAnnotationQuickstart.html", | ||
| sourceUrl: | ||
| "https://raw.githubusercontent.com/hed-standard/hed-resources/main/docs/source/HedAnnotationQuickstart.md", |
Collaborator
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{
"docs_url": "https://www.hedtags.org/hed-resources/",
"doc_type": "sphinx",
"has_sources_dir": false,
"total_pages": 28,
"pages": [
{
"docname": "BidsAnnotationQuickstart",
"title": "BIDS annotation quickstart",
"html_url": "https://www.hedtags.org/hed-resources/BidsAnnotationQuickstart.html",
"source_filename": "BidsAnnotationQuickstart.rst"
},
{
"docname": "CTaggerGuiTaggingTool",
"title": "CTagger GUI tagging tool",
"html_url": "https://www.hedtags.org/hed-resources/CTaggerGuiTaggingTool.html",
"source_filename": "CTaggerGuiTaggingTool.rst"
},
{
"docname": "DocumentationSummary",
"title": "Documentation summary",
"html_url": "https://www.hedtags.org/hed-resources/DocumentationSummary.html",
"source_filename": "DocumentationSummary.rst"
},
{
"docname": "HEDSubmissionToINCF",
"title": "HED INCF Standard Application",
"html_url": "https://www.hedtags.org/hed-resources/HEDSubmissionToINCF.html",
"source_filename": "HEDSubmissionToINCF.rst"
},
{
"docname": "HedAndEEGLAB",
"title": "HED and EEGLAB",
"html_url": "https://www.hedtags.org/hed-resources/HedAndEEGLAB.html",
"source_filename": "HedAndEEGLAB.rst"
},
{
"docname": "HedAnnotationInNWB",
"title": "HED annotation in NWB",
"html_url": "https://www.hedtags.org/hed-resources/HedAnnotationInNWB.html",
"source_filename": "HedAnnotationInNWB.rst"
},
{
"docname": "HedAnnotationQuickstart",
"title": "HED annotation quickstart",
"html_url": "https://www.hedtags.org/hed-resources/HedAnnotationQuickstart.html",
"source_filename": "HedAnnotationQuickstart.rst"
},
{
"docname": "HedAnnotationSemantics",
"title": "HED annotation semantics",
"html_url": "https://www.hedtags.org/hed-resources/HedAnnotationSemantics.html",
"source_filename": "HedAnnotationSemantics.rst"
},
{
"docname": "HedConditionsAndDesignMatrices",
"title": "HED conditions and design matrices",
"html_url": "https://www.hedtags.org/hed-resources/HedConditionsAndDesignMatrices.html",
"source_filename": "HedConditionsAndDesignMatrices.rst"
},
{
"docname": "HedGovernance",
"title": "HED governance",
"html_url": "https://www.hedtags.org/hed-resources/HedGovernance.html",
"source_filename": "HedGovernance.rst"
},
{
"docname": "HedHistory",
"title": "Brief history of HED",
"html_url": "https://www.hedtags.org/hed-resources/HedHistory.html",
"source_filename": "HedHistory.rst"
},
{
"docname": "HedJavascriptTools",
"title": "HED JavaScript tools",
"html_url": "https://www.hedtags.org/hed-resources/HedJavascriptTools.html",
"source_filename": "HedJavascriptTools.rst"
},
{
"docname": "HedMatlabTools",
"title": "HED MATLAB tools",
"html_url": "https://www.hedtags.org/hed-resources/HedMatlabTools.html",
"source_filename": "HedMatlabTools.rst"
},
{
"docname": "HedOnlineTools",
"title": "HED online tools",
"html_url": "https://www.hedtags.org/hed-resources/HedOnlineTools.html",
"source_filename": "HedOnlineTools.rst"
},
{
"docname": "HedPythonTools",
"title": "HED Python tools",
"html_url": "https://www.hedtags.org/hed-resources/HedPythonTools.html",
"source_filename": "HedPythonTools.rst"
},
{
"docname": "HedRemodelingQuickstart",
"title": "HED remodeling quickstart",
"html_url": "https://www.hedtags.org/hed-resources/HedRemodelingQuickstart.html",
"source_filename": "HedRemodelingQuickstart.rst"
},
{
"docname": "HedRemodelingTools",
"title": "HED remodeling tools",
"html_url": "https://www.hedtags.org/hed-resources/HedRemodelingTools.html",
"source_filename": "HedRemodelingTools.rst"
},
{
"docname": "HedSchemaDevelopersGuide",
"title": "HED schema developer\u2019s guide",
"html_url": "https://www.hedtags.org/hed-resources/HedSchemaDevelopersGuide.html",
"source_filename": "HedSchemaDevelopersGuide.rst"
},
{
"docname": "HedSchemas",
"title": "HED schemas",
"html_url": "https://www.hedtags.org/hed-resources/HedSchemas.html",
"source_filename": "HedSchemas.rst"
},
{
"docname": "HedSearchGuide",
"title": "HED search guide",
"html_url": "https://www.hedtags.org/hed-resources/HedSearchGuide.html",
"source_filename": "HedSearchGuide.rst"
},
{
"docname": "HedSummaryGuide",
"title": "HED summary guide",
"html_url": "https://www.hedtags.org/hed-resources/HedSummaryGuide.html",
"source_filename": "HedSummaryGuide.rst"
},
{
"docname": "HedTestDatasets",
"title": "HED test datasets",
"html_url": "https://www.hedtags.org/hed-resources/HedTestDatasets.html",
"source_filename": "HedTestDatasets.rst"
},
{
"docname": "HedValidationGuide",
"title": "HED validation guide",
"html_url": "https://www.hedtags.org/hed-resources/HedValidationGuide.html",
"source_filename": "HedValidationGuide.rst"
},
{
"docname": "HowCanYouUseHed",
"title": "How can you use HED?",
"html_url": "https://www.hedtags.org/hed-resources/HowCanYouUseHed.html",
"source_filename": "HowCanYouUseHed.rst"
},
{
"docname": "IntroductionToHed",
"title": "Introduction to HED",
"html_url": "https://www.hedtags.org/hed-resources/IntroductionToHed.html",
"source_filename": "IntroductionToHed.rst"
},
{
"docname": "UnderstandingHedVersions",
"title": "Understanding HED versions",
"html_url": "https://www.hedtags.org/hed-resources/UnderstandingHedVersions.html",
"source_filename": "UnderstandingHedVersions.rst"
},
{
"docname": "WhatsNew",
"title": "What\u2019s new?",
"html_url": "https://www.hedtags.org/hed-resources/WhatsNew.html",
"source_filename": "WhatsNew.rst"
},
{
"docname": "index",
"title": "HED resources",
"html_url": "https://www.hedtags.org/hed-resources/index.html",
"source_filename": "index.rst"
}
]
}
which shows deficiency that sources are not discovered!
6 tasks
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Summary
Implements a new HED (Hierarchical Event Descriptors) assistant following the established BIDS assistant pattern. Provides technical guidance on HED annotation based on official HED specification and resources documentation.
Features
Implementation
Follows BIDS assistant pattern exactly:
Testing
Files Modified
Files Added
Benefits