Updated the documentation

Author: VisLab

docs/api/errors.md

@@ -4,54 +4,113 @@ Error handling and exception classes for HED validation and processing.
 
 ## Exception Classes
 
+Core exception classes for HED-related errors.
+
 ### HedFileError
 
 ::: hed.errors.exceptions.HedFileError
     options:
-      show_source: true
+      show_source: false
+      heading_level: 4
 
 ### HedExceptions
 
 ::: hed.errors.exceptions.HedExceptions
     options:
-      show_source: true
+      show_source: false
+      heading_level: 4
 
 ## Error Reporting
 
+Classes for collecting, managing, and reporting validation errors.
+
 ### ErrorHandler
 
 ::: hed.errors.error_reporter.ErrorHandler
     options:
-      show_source: true
+      show_source: false
+      heading_level: 4
+
+### Error Reporting Functions
+
+::: hed.errors.error_reporter.get_printable_issue_string
+    options:
+      show_source: false
+      heading_level: 4
+
+::: hed.errors.error_reporter.sort_issues
+    options:
+      show_source: false
+      heading_level: 4
+
+::: hed.errors.error_reporter.replace_tag_references
+    options:
+      show_source: false
+      heading_level: 4
 
 ### ErrorContext
 
 ::: hed.errors.error_types.ErrorContext
     options:
-      show_source: true
-
-## Error Types
+      show_source: false
+      heading_level: 4
 
 ### ErrorSeverity
 
 ::: hed.errors.error_types.ErrorSeverity
     options:
-      show_source: true
+      show_source: false
+      heading_level: 4
+
+## Error Types
+
+Specific error categories for different types of validation issues.
 
 ### ValidationErrors
 
 ::: hed.errors.error_types.ValidationErrors
     options:
-      show_source: true
+      show_source: false
+      heading_level: 4
+
+### SchemaErrors
+
+::: hed.errors.error_types.SchemaErrors
+    options:
+      show_source: false
+      heading_level: 4
+
+### SchemaWarnings
+
+::: hed.errors.error_types.SchemaWarnings
+    options:
+      show_source: false
+      heading_level: 4
 
 ### SidecarErrors
 
 ::: hed.errors.error_types.SidecarErrors
     options:
-      show_source: true
+      show_source: false
+      heading_level: 4
+
+### ColumnErrors
+
+::: hed.errors.error_types.ColumnErrors
+    options:
+      show_source: false
+      heading_level: 4
+
+### DefinitionErrors
+
+::: hed.errors.error_types.DefinitionErrors
+    options:
+      show_source: false
+      heading_level: 4
 
-## Schema Error Messages
+### TemporalErrors
 
-::: hed.errors.schema_error_messages
+::: hed.errors.error_types.TemporalErrors
     options:
-      show_source: true
+      show_source: false
+      heading_level: 4

docs/api/index.md

@@ -7,64 +7,56 @@ This section provides comprehensive documentation for all HED Python tools modul
 ### [Models](models.md)
 Core data models for working with HED data:
 
-- **HedString**: Represents and validates HED annotation strings
-- **HedTag**: Individual HED tag manipulation
-- **HedGroup**: Grouped HED annotations
-- **Sidecar**: BIDS sidecar file handling
-- **TabularInput**: Spreadsheet and tabular data processing
+- **Core Models**: HedString, HedTag, HedGroup, DefinitionDict, DefinitionEntry
+- **Input Models**: BaseInput, TabularInput, SpreadsheetInput, TimeseriesInput, Sidecar
+- **Query Models**: QueryHandler and query service functions
+- **Utility Models**: ColumnMapper, ColumnMetadata, DataFrame utilities
 
 ### [Schema](schema.md)
 HED schema management and validation:
 
-- **HedSchema**: Main schema class for loading and querying schemas
-- **HedSchemaIO**: Schema input/output operations
-- **SchemaComparer**: Compare different schema versions
+- **Core Schema**: HedSchema, HedSchemaEntry, HedSchemaGroup, HedSchemaSection
+- **Schema I/O**: Schema loading, caching, and file operations
+- **Schema Utilities**: Comparison tools, validation utilities, compliance checking
 
 ### [Validator](validator.md)
 Validation tools and error handling:
 
-- **HedValidator**: Main validation engine
-- **ErrorReporter**: Error collection and reporting
-- **ValidationContext**: Validation state management
+- **Core Validators**: HedValidator, SidecarValidator
+- **Specialized Validators**: Definition validator, onset validator, spreadsheet validator
 
 ### [Tools](tools.md)
-Utility tools and scripts:
+Utility tools and data transformation operations:
 
-- **BidsTabularSummary**: BIDS dataset analysis
-- **ReorderColumns**: Spreadsheet manipulation
-- **TagCompareUtil**: Tag comparison utilities
+- **Analysis Tools**: TabularSummary, annotation utilities, tag counting
+- **Remodeling Operations**: Comprehensive set of data transformation operations
+- **Remodeling Utilities**: Remodeler, backup manager, dispatcher
 
 ### [Errors](errors.md)
 Error handling and exception classes:
 
-- **HedFileError**: File-related errors
-- **HedExceptions**: General HED exceptions
-- **ErrorMessages**: Error message definitions
+- **Exception Classes**: HedFileError, HedExceptions
+- **Error Reporting**: ErrorHandler, ErrorReporter, validation context
+- **Error Messages**: Comprehensive error message definitions
 
 ## Quick Reference
 
-### Loading and Using Schemas
+### Loading Schemas
 
 ::: hed.load_schema
     options:
-      show_source: true
+      show_source: false
+      heading_level: 3
 
-### Basic Validation
-
-::: hed.HedString
+::: hed.load_schema_version
     options:
-      show_source: true
-      members:
-        - __init__
-        - validate
-        - remove_definitions
+      show_source: false
+      heading_level: 3
 
-### Working with BIDS Data
+### Working with HED Strings
 
-::: hed.models.Sidecar
+::: hed.HedString
     options:
-      show_source: true
-      members:
-        - __init__
-        - validate
-        - extract_definitions
+      show_source: false
+      heading_level: 3
+      members: []

docs/api/models.md

@@ -2,56 +2,150 @@
 
 Core data models for working with HED data structures.
 
-## HedString
+## Core Models
+
+The fundamental data structures for HED annotations and tags.
+
+### HedString
 
 ::: hed.models.hed_string.HedString
     options:
-      show_source: true
+      show_source: false
+      heading_level: 4
 
-## HedTag
+### HedTag
 
 ::: hed.models.hed_tag.HedTag
     options:
-      show_source: true
+      show_source: false
+      heading_level: 4
 
-## HedGroup
+### HedGroup
 
 ::: hed.models.hed_group.HedGroup
     options:
-      show_source: true
+      show_source: false
+      heading_level: 4
 
-## Sidecar
+### DefinitionDict
 
-::: hed.models.sidecar.Sidecar
+::: hed.models.definition_dict.DefinitionDict
+    options:
+      show_source: false
+      heading_level: 4
+
+### DefinitionEntry
+
+::: hed.models.definition_entry.DefinitionEntry
+    options:
+      show_source: false
+      heading_level: 4
+
+## Input Models
+
+Classes for handling different types of input data formats.
+
+### BaseInput
+
+::: hed.models.base_input.BaseInput
     options:
-      show_source: true
+      show_source: false
+      heading_level: 4
 
-## TabularInput
+### TabularInput
 
 ::: hed.models.tabular_input.TabularInput
     options:
-      show_source: true
+      show_source: false
+      heading_level: 4
 
-## SpreadsheetInput
+### SpreadsheetInput
 
 ::: hed.models.spreadsheet_input.SpreadsheetInput
     options:
-      show_source: true
+      show_source: false
+      heading_level: 4
 
-## BaseInput
+### TimeseriesInput
 
-::: hed.models.base_input.BaseInput
+::: hed.models.timeseries_input.TimeseriesInput
     options:
-      show_source: true
+      show_source: false
+      heading_level: 4
 
-## ColumnMapper
+### Sidecar
+
+::: hed.models.sidecar.Sidecar
+    options:
+      show_source: false
+      heading_level: 4
+
+## Query Models
+
+Classes for searching and querying HED data.
+
+### QueryHandler
+
+::: hed.models.query_handler.QueryHandler
+    options:
+      show_source: false
+      heading_level: 4
+
+### Query Service Functions
+
+::: hed.models.query_service.get_query_handlers
+    options:
+      show_source: false
+      heading_level: 4
+
+::: hed.models.query_service.search_hed_objs
+    options:
+      show_source: false
+      heading_level: 4
+
+## Utility Models
+
+Support classes for data management and processing.
+
+### ColumnMapper
 
 ::: hed.models.column_mapper.ColumnMapper
     options:
-      show_source: true
+      show_source: false
+      heading_level: 4
 
-## DefinitionDict
+### ColumnMetadata
 
-::: hed.models.definition_dict.DefinitionDict
+::: hed.models.column_metadata.ColumnMetadata
+    options:
+      show_source: false
+      heading_level: 4
+
+### ColumnType
+
+::: hed.models.column_metadata.ColumnType
+    options:
+      show_source: false
+      heading_level: 4
+
+### DataFrame Utilities
+
+::: hed.models.df_util.convert_to_form
+    options:
+      show_source: false
+      heading_level: 4
+
+::: hed.models.df_util.shrink_defs
+    options:
+      show_source: false
+      heading_level: 4
+
+::: hed.models.df_util.expand_defs
+    options:
+      show_source: false
+      heading_level: 4
+
+::: hed.models.df_util.process_def_expands
     options:
-      show_source: true
+      show_source: false
+      heading_level: 4