Merge pull request hed-standard#1106 from hed-standard/main

Updating develop with latest version of main

Author: VisLab

.github/dependabot.yml

@@ -1,18 +1,18 @@
-version: 2
-updates:
-  - package-ecosystem: "github-actions"
-    directory: "/"
-    target-branch: "develop"
-    schedule:
-      interval: "weekly"
-  - package-ecosystem: "pip"
-    directory: "/"
-    target-branch: "develop"
-    schedule:
-      interval: "weekly"
-
-  - package-ecosystem: gitsubmodule
-    schedule:
-        interval: "daily"
-    target-branch: "develop"
-    directory: /
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    target-branch: "main"
+    schedule:
+      interval: "weekly"
+  - package-ecosystem: "pip"
+    directory: "/"
+    target-branch: "main"
+    schedule:
+      interval: "weekly"
+
+  - package-ecosystem: gitsubmodule
+    schedule:
+        interval: "daily"
+    target-branch: "main"
+    directory: /

.github/workflows/ci_cov.yaml

@@ -74,7 +74,7 @@ jobs:
       # Upload coverage to qlty
       - name: Upload coverage to qlty
         if: needs.check-secret.outputs.secrets-exist == 'true'
-        uses: qltysh/qlty-action/coverage@v1
+        uses: qltysh/qlty-action/coverage@v2
         with:
           token: ${{ secrets.QLTY_COVERAGE_TOKEN }}
           files: coverage.xml

.github/workflows/ci_windows.yaml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       matrix:
         platform: [windows-latest]
-        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     runs-on: ${{ matrix.platform }}
 

.github/workflows/docs.yml

@@ -64,6 +64,8 @@ jobs:
   deploy:
     # This job depends on the 'build' job completing successfully
     needs: build
+    # Only deploy when pushing to main branch, not on pull requests
+    if: github.event_name == 'push' && github.ref == 'refs/heads/main'
     permissions:
       pages: write
       id-token: write

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: []