Tags

Release v2.3.1: Complete type checking fixes and responsive UI improvements

- Fixed all type checking errors in test_bigwig_validation.py
- Enhanced type narrowing with proper assert statements for mypy compatibility
- Fixed HTTPError instantiation with proper EmailMessage headers
- Removed duplicate test files for code consistency

- Fixed responsive project info widget overlapping navigation on narrow screens
- Enhanced z-index handling (1000-1001) for proper widget layering
- Added mobile-friendly modal behavior with close buttons and backdrop
- Implemented smart responsive breakpoints for all screen sizes

- Updated all version references to v2.3.1 consistently across:
  - jbrowse_batch_tracks.py (__version__)
  - README.md (version badge)
  - docs/index.md (version info)
  - mkdocs.yml (project info)

- Updated CHANGELOG.md and docs/changelog.md with comprehensive v2.3.1 entries
- Maintained consistent documentation and version info across all files

- Standardized type checking patterns across entire test suite
- Improved test file organization and naming consistency
- Enhanced code quality and maintainability

Release v2.2.2: Documentation Structure Updates

This release focuses on improving documentation accuracy and project usability:

- Updated docs/usage.md with comprehensive current project structure
- Corrected all file references to match actual files in the project
- Updated docs/testing.md with accurate test file listings
- Removed references to non-existent test files
- Added references to existing files

- Added changelog maintenance instructions to docs/contributing.md
- Synchronized docs/changelog.md with root CHANGELOG.md for consistency
- Documented platform-specific commands for maintaining changelog sync

- Verified all mentioned directories exist (tests/, example-data/, docs/, demos/, reports/, archive/)
- Confirmed all referenced test files exist in the actual project structure
- Updated test structure diagrams to reflect current organization

No breaking changes - this version improves documentation without affecting core functionality.

v2.2.1 - Test Organization and Code Cleanup

- Reorganize blank line handling tests into proper unittest structure
- Move test files to appropriate directories (tests/ and example-data/)
- Remove unrelated test code from duplicate handling tests
- Remove debug scripts replaced by proper unit tests
- Maintain separation of concerns between test modules
- All tests pass with proper organization

Release v2.2.0: Track-Type Specific Duplicate Handling

Enhanced duplicate detection system:
- Quantitative tracks: check track_name duplicates only
- MultiQuantitative tracks: check subtrack_name duplicates within same track_name
- Cross-track subtracks with identical names are allowed (no conflict)
- New DuplicateSubtrackError exception for granular error handling
- Comprehensive test suite and updated documentation

Version 2.1.1: JBrowse2 URI Path Compatibility Fix

- Fixed JBrowse2 track loading issue with file:/// URI format
- Improved compatibility with JBrowse2 interface
- Updated all documentation and examples
- Enhanced track loading reliability
- Consolidated changelog to docs/ directory
- Fixed documentation formatting issues
- Updated all documentation references

JBrowse2 Batch Track Submission v2.1.0

🎯 Key Features:
- Three duplicate handling policies: skip, overwrite, interactive
- Removed --allow-duplicates to prevent JBrowse2 display issues
- Comprehensive error handling with severity levels
- Custom exception system for duplicate management

🔧 Technical Improvements:
- Organized test suite with comprehensive coverage
- Repository cleanup and archive structure
- Enhanced logging and progress reporting
- Version management and release tagging

📚 Documentation & Testing:
- Complete duplicate handling documentation
- Updated user guides and API documentation with CLI options
- Fixed TSV example formatting in usage documentation
- Comprehensive test suite with verification scripts

This release improves reliability, user experience, and maintainability.

Version 1.0.0: Enhanced CLI with argparse, backup and dry-run features

Version 2.0.0: Major release with ExecutionReporter system, comprehensive documentation, repository organization, and enhanced testing