Tags give the ability to mark specific points in history as being important
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v2.5.5
2dc2db80 · ·v2.5.5 - Interface Simplification Release Major Changes: - Simplified reporting interface with single --report-output argument - Removed redundant --generate-report and --report-dir arguments - Automatic directory creation based on user-specified paths - Enhanced documentation with v2.5.5 examples Benefits: - More intuitive user experience - Reduced complexity for automation scripts - Maintains full backward compatibility - Comprehensive validation and testing Complete documentation updates across all relevant files
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v2.5.4.1
3ac00e52 · ·Release v2.5.4.1: Documentation Organization & Project Cleanup 📚 DOCUMENTATION IMPROVEMENTS: - Comprehensive documentation reorganization with proper directory structure - Created docs/releases/ folder for version-specific documentation - Added docs/README.md as comprehensive documentation index - Moved development documentation to docs/ for better organization - Enhanced documentation navigation and cross-references 🗂️ PROJECT STRUCTURE: - Clean separation of user documentation vs development documentation - Centralized release documentation in organized folders - Updated .gitignore patterns for better maintenance - Improved project organization following best practices 🔧 VERSION MANAGEMENT: - Updated version to 2.5.4 in main script - Updated README.md badges and version information - Added v2.5.4 release information to main CHANGELOG.md - Enhanced project metadata and documentation ✅ BENEFITS: - Easier navigation for users and contributors - Clear documentation hierarchy and organization - Better maintenance workflow for future releases - Maintained backward compatibility for existing documentation links This patch release improves project organization and documentation without changing core functionality.
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v2.5.4
c06dc4f3 · ·Release v2.5.4: Fix Report Generation Path Handling & Dependencies 🐛 CRITICAL BUG FIXES: - Fixed ExecutionReporter path handling for custom --report-output locations - Fixed silent report generation failures due to missing plotly dependency - Enhanced path logic to support absolute paths and subdirectories - Fixed duplicate return statement in execution_reporter.py 🔧 IMPROVEMENTS: - Automatic parent directory creation for custom report paths - Enhanced method documentation and error handling - Added plotly>=5.0.0 to requirements.txt ✅ COMPATIBILITY: - Fully backward compatible with existing workflows - New capability: Custom report output paths - Comprehensive testing validates all scenarios 📁 FILES CHANGED: - execution_reporter.py: Enhanced path handling logic - requirements.txt: Added plotly dependency (in previous commit) - Added comprehensive documentation (CHANGELOG_v2.5.4.md, RELEASE_NOTES_v2.5.4.md) This release resolves the user-reported issue where --generate-report with --report-output wasn't creating report files.
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v2.5.2-deprecated
c19d2a79 · ·Version 2.5.2 - DEPRECATED - DO NOT USE ❌ DEPRECATED: This version contains incorrect JBrowse2 track types ❌ Issues with this version: - Uses non-existent LinearWiggleTrack instead of QuantitativeTrack - Incorrect defaultRendering 'line' instead of 'xyplot' for MultiQuantitativeTrack - Complex displays arrays instead of direct track settings - Configuration not properly recognized by JBrowse2 browser ✅ USE v2.5.3 INSTEAD - Contains all fixes and proper JBrowse2 compatibility This tag is preserved for historical reference only.
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v2.5.3
e2c39078 · ·Version 2.5.3 - Complete Track Configuration Fix ✅ FINAL VERSION - All JBrowse2 Compatibility Issues Resolved ✅ Critical fixes for proper JBrowse2 track configuration: 🔧 Core Corrections: - Fixed track types: QuantitativeTrack and MultiQuantitativeTrack (not LinearWiggleTrack) - Corrected rendering: defaultRendering 'xyplot' for MultiQuantitativeTrack - Simplified structure: Direct track property application (no displays arrays) - JBrowse2 compatible: Settings properly recognized and displayed in browser 🎯 User Requirements FULFILLED: ✅ XYPlotRenderer for multiquantitative tracks with xyplot rendering ✅ Lighter colors for quantitative tracks (Sky Blue #87CEEB) ✅ Automatic configuration loading from script directory ✅ Full JBrowse2 browser compatibility and display 📚 Complete documentation updates included for all features. This version ensures XYPlotRenderer and lighter colors are properly visible and functional in JBrowse2 browser interface.
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v2.5.1
9449320c · ·Release v2.5.1: Enhanced default configuration loading Configuration Loading Improvements: - TrackConfigManager prioritizes script directory over current directory - Bundled track_config.json automatically loaded for better defaults - Improved user experience with automatic XYPlotRenderer and lighter colors Documentation Updates: - Updated track configuration guide and API reference - Clarified configuration file priority order - Enhanced help text for --track-config parameter This release provides a smoother out-of-the-box experience by ensuring the optimized default configuration travels with the script installation.
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v2.5.0
1df8b4c4 · ·Release v2.5.0: JSON-Based Track Configuration System Major new features: - JSON-based track configuration system for customizing appearance - XYPlotRenderer as default for multiquantitative tracks - Lighter color schemes for better readability - Configurable renderer types and color palettes - Assembly and category-specific configuration overrides - Command-line integration with --track-config parameter - Complete backward compatibility with existing workflows - Fixed --version command display New files: - track_config.json: Default configuration with user-requested settings - track_config_manager.py: Configuration management system - docs/track-configuration.md: Complete user guide - docs/api-reference.md: API documentation - VERSION_2.5.0_SUMMARY.md: Release summary Addresses user requests for: - XYPlotRenderer for multiquantitative tracks - Lighter default colors (#87CEEB Sky Blue, etc.) - JSON-configurable track options This release maintains full backward compatibility while adding powerful new customization capabilities through optional JSON configuration.
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v2.4.0
f7f4f636 · ·Release v2.4.0: Complete Track Management Toolkit Major release introducing comprehensive track removal capabilities: - New jbrowse_remove_tracks.py tool with selective and complete removal modes - Complete track lifecycle management (addition + removal) - Comprehensive documentation and workflow examples - Enhanced testing coverage and example data - File reorganization and improved project structure This release completes the JBrowse2 track management toolkit with production-ready track removal functionality, comprehensive safety features, and complete documentation.
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v2.3.1
ed050587 · ·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
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v2.2.2
1df10f89 · ·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.
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v2.2.1
33fb9cd7 · ·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
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v2.2.0
66f638be · ·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
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v2.1.1
71da047b · ·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
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v2.1.0
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.
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v2.0.0
fb47eb5f · ·Version 2.0.0: Major release with ExecutionReporter system, comprehensive documentation, repository organization, and enhanced testing