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Updated CHANGELOG in preparation of release 0.9.0
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‎CHANGELOG.md‎

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````markdown
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Release 0.9.0 January 22, 2026
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The main purpose of this release is to clean up the CLI for the hedtools and to improve the documentation in preparation for release of 1.0.0, which will be a breaking release.
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## Major changes
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### Command-line interface (CLI) overhaul
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**Complete CLI redesign with Git-Style commands**
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- Introduced unified `hedpy` command-line interface with git-style subcommand structure
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- Replaced legacy standalone scripts with organized command groups: `validate`, `schema`, `extract`
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- Added comprehensive help system with detailed command documentation
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- Implemented click-option-group for organized command options
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**New commands:**
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- `hedpy validate bids-dataset` - BIDS dataset validation
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- `hedpy validate string` - HED string validation
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- `hedpy validate sidecar` - JSON sidecar validation
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- `hedpy validate tabular` - TSV file validation
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- `hedpy schema validate` - Schema file validation
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- `hedpy schema convert` - Schema format conversion
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- `hedpy schema add-ids` - HED ID management
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- `hedpy extract bids-sidecar` - Sidecar template extraction
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- `hedpy extract tabular-summary` - Tabular file summarization
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**Enhanced output options:**
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- Multiple output formats: text, json, json_pp (pretty-printed JSON with metadata)
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- Configurable error limiting per error type
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- File-based and per-error error counting options
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- Comprehensive logging configuration with file output support
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### Documentation improvements
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**Major documentation restructuring**
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- Complete rewrite of user guide with comprehensive examples and workflows
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- Added detailed Jupyter notebook documentation section
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- Created extensive CLI documentation with command examples
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- Improved API reference organization with clearer section headers
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- Enhanced introduction page with quick start examples
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- Added troubleshooting section with common issues and solutions
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- Updated the RELEASE_GUIDE to better reflect current release process
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**New documentation features:**
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- Sidebar quick links for easy navigation
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- Custom CSS styling for improved readability
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- Dark mode support with proper color theming
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- Brand customization with project logo and name
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- Better code block formatting and syntax highlighting
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- Comprehensive examples for all major workflows
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### Jupyter notebook examples
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**New example notebooks (examples/ directory)**
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- `extract_json_template.ipynb` - Generate JSON sidecar templates
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- `find_event_combinations.ipynb` - Find unique value combinations
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- `merge_spreadsheet_into_sidecar.ipynb` - Merge edited annotations
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- `sidecar_to_spreadsheet.ipynb` - Convert JSON to spreadsheet format
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- `summarize_events.ipynb` - Summarize event file contents
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- `validate_bids_dataset.ipynb` - Validate BIDS datasets
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- `validate_bids_dataset_with_libraries.ipynb` - Validate with library schemas
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- `validate_bids_datasets.ipynb` - Batch validate multiple datasets
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- `validate_bids_dataset_nondefault. ipynb` - Non-standard validation scenarios
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**Notebook infrastructure:**
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- Added comprehensive README for notebooks with usage instructions
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- Created optional dependencies group for Jupyter support
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- Added notebook testing framework for validation
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### Core functionality enhancements
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**Validation improvements:**
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- Enhanced placeholder validation with units (e.g., "# m-per-s^2")
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- Fixed unit class validation for placeholders with units
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- Improved error reporting with better categorization
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- Added support for --no-log option to disable all logging
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**TabularSummary Enhancements:**
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- Added categorical limit feature to prevent memory issues with high-cardinality columns
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- Implemented overflow column tracking for truncated summaries
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- Added categorical counts metadata (total values and file counts)
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- Improved summary statistics and reporting
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**Schema processing:**
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- Enhanced schema validation error messages with specification links
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- Fixed schema attribute inheritance handling
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- Improved JSON schema format support
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- Updated conversion factor validation
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### Script and utility improvements
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**New scripts:**
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- `hed/scripts/validate_hed_string.py` - Standalone HED string validation
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- `hed/scripts/validate_hed_sidecar.py` - Standalone sidecar validation
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- `hed/scripts/validate_hed_tabular.py` - Standalone tabular file validation
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- `hed/scripts/extract_tabular_summary.py` - Non-BIDS tabular summarization
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- `hed/scripts/script_utils.py` - Shared utility functions for scripts
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**Script uilities:**
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- Centralized logging setup across all scripts
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- Standardized validation result formatting
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- Consistent error handling and reporting
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- Improved argument parsing with organized option groups
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### Dependencies and requirements
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**Updated Dependencies:**
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- Added `click-option-group>=0.5.0` for CLI option organization
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- Updated `wordcloud` from 1.9.4 to 1.9.5
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- Updated `black` to >=26.1.0 with Jupyter support
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- Added `mdformat>=0.7.0` and `mdformat-myst>=0.1.5` for markdown formatting
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- Updated Sphinx and documentation dependencies
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**New Optional Dependency Groups:**
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- `examples` - Jupyter notebook support (jupyter, notebook, nbformat, ipykernel)
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- Updated `docs` group with version constraints
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- Enhanced `dev` group with markdown formatting tools
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### Testing enhancements
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**Schema test data:**
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- Added extensive JSON test data for schema validation
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- New test files for schema attribute validation
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- Tests for conversion factors, HED IDs, unit classes, value classes
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- Tests for character validation and deprecation handling
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- Tests for library schema attributes
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**Test organization:**
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- Improved test structure with categorized error cases
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- Added common causes and correction strategies to test metadata
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- Enhanced test documentation with specification references
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- Moved JSON test references from the hed-specification repository to the hed-tests repository
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### Documentation files
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**Updated documentation:**
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- Comprehensive CHANGELOG.md updates
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- Enhanced CONTRIBUTING.md with detailed workflows
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- Improved README. md with better examples and structure
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- Updated RELEASE_GUIDE.md with detailed release procedures
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**Configuration files:**
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- Added `.lycheeignore` for link checker exclusions
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- Added `lychee.toml` for link validation configuration
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- Enhanced `.gitignore` with additional patterns
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- Updated workflow configurations for GitHub Actions
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## GitHub actions and CI/CD
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### Workflow updates
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**Enhanced CI pipeline:**
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- Updated cache actions from v4 to v5 across all workflows
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- Changed default branch references from `develop` to `main`
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- Renamed and reorganized workflow files (. yml → .yaml)
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- Improved Sphinx documentation build workflow
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**New workflows:**
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- `links. yaml` - Lychee link checker for documentation (weekly schedule)
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- `mdformat.yaml` - Markdown formatting validation
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- `notebook_tests.yaml` - Jupyter notebook validation
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- `ruff.yaml` - Python linting with Ruff
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**Workflow improvements:**
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- Updated codespell workflow to use main branch
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- Enhanced documentation deployment workflow
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- Added proper artifact handling for GitHub Pages
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- Improved test isolation and parallel execution
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## File organization and structure
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### Repository structure changes
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**Removed:**
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- Removed `spec_tests/hed-specification` submodule (replaced with hed-tests)
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- Removed remodeling CLI commands (moved to separate repository)
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**Added:**
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- New `examples/` directory with Jupyter notebooks and README
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- New `hed/scripts/script_utils.py` for shared utilities
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- New validation scripts for string, sidecar, and tabular files
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- New extract script for non-BIDS tabular summaries
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**Updated:**
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- Moved documentation assets from `docs/assets/` to `docs/_static/`
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- Enhanced documentation structure with better organization
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- Improved test data organization in spec_tests/
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### Code quality and formatting
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**Black formatting:**
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- Applied Black code formatter across entire codebase
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- Updated Black configuration for Python 3.14 support
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- Enhanced exclusion patterns for auto-generated files
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**Ruff linting:**
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- Added comprehensive Ruff configuration
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- Implemented linting rules for code quality
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- Added automated linting in CI pipeline
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**Markdown formatting:**
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- Added mdformat for consistent markdown styling
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- Configured myst-parser support
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- Automated markdown checking in CI
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## Bug fixes and minor improvements
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### Schema handling
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- Fixed MediaWiki → MEDIAWIKI naming consistency
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- Improved schema format detection and conversion
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- Enhanced schema attribute validation
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- Fixed inheritance handling for schema attributes
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### Validation
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- Fixed unit validation for placeholders with units
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- Improved error message clarity and documentation links
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- Fixed definition extraction from sidecars
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- Enhanced sidecar validation error reporting
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### Error reporting
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- Updated documentation link format in error messages
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- Improved error categorization and grouping
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- Added error iteration utility (`iter_errors`)
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- Enhanced printable issue formatting
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### Miscellaneous
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- Fixed various typos and formatting issues
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- Improved code comments and docstrings
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- Enhanced type hints and error handling
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- Cleaned up deprecated code patterns
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## Breaking changes
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**CLI command changes:**
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- Legacy commands are now deprecated (still work but show warnings)
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- Recommended migration to new `hedpy` command structure
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- Some command-line argument names have changed for consistency
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**Python version:**
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- Minimum Python version remains 3.10
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- Added support for Python 3.14
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## Migration guide
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### CLI Migration
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```bash
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# Old (deprecated)
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validate_bids /path/to/dataset
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# New (recommended)
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hedpy validate bids-dataset /path/to/dataset
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```
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### Script Imports
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```python
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# Validation functions remain unchanged
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from hed import HedString, load_schema_version, BidsDataset
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# New utility imports available
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from hed.errors import iter_errors
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from hed.scripts.script_utils import format_validation_results
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```
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Release 0.8.1 December 9, 2025
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The primary purpose of this release was to correct the JSON format for HED schemas so that it would accurately distinguish between inherited and non-inherited attributes. The documentation layout was also improved with quick links.

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