This release is one of the biggest to date. It modernizes the entire stack, improves performance across all tools, introduces much faster and fully asynchronous job handling for BLAST and tree building, upgrades to Python 3.14, and delivers major UX improvements throughout the application.
New Features
Improved Tag System
- Tags now support Markdown files
- Magic genome tags enabled in Compare Genes.
- Tag right-click menu fixed and improved.
- Added missing data-tag attributes.
Markdown Enhancements
- Markdown editor added to all tool pages.
- Tag markdown rendering improvements.
Speed improvements for BLAST & Trees
- New fast BLAST tool interface integrated.
- BLAST searches and tree-building tasks can now run fully in the background
Redis Integration
- Added Redis service and switched Huey backend from SQLite -> Redis.
- Improved job stability and parallelism.
- Graceful handling of multi-container setups and Redis permissions.
Frontend & UX Improvements
- Updated colors, fonts, and design elements to align with Abrinca design guidelines.
- More intuitive navigation bar
- Made tool settings easier accessible
Genome, Annotation & File Browser Improvements
- GenomeFilter improvements.
- Genome page load time improved.
- File browser shows more files in-browser instead of attachments.
Performance Enhancements
- Major performance improvements across genome, BLAST, and taxid views.
- Optimized JavaScript and HTML templates.
- Reduced unnecessary refreshes.
- Faster genome detail rendering.
- Moved annotation and genome lookups to more efficient providers.
Infrastructure, Deployment & Backend
Python 3.14 Upgrade
- Fully upgraded the application to Python 3.14.
- Updated dependencies accordingly.
Database & Storage
- Graceful shutdown for PostgreSQL and services on container exit.
- Fixed genome upload logic.
- Improved cache settings for the downloader.
- Optimized queue scheduling to avoid race conditions.
Logging
- Unified logging across the application
- Improved logging in manage_arx.
Testing
- Optimized testing setup
- More diverse data used in tests to catch edge cases.
Bug fixes
BLAST
- Corrected gene/annotation species display.
- Improved BLAST-related error messages.
Trees
- Fix "Copy to clipboard".
- Fix behavioral inconsistencies.
- Fix color and background issues.
Tags
- Fix disappearing tags in genome sorting.
- Fix tag colors.
- Fix ineffective tag right-click line.
Annotation Matrix
- Correct species shown.
- Fix annotation menu.
- Fix matrix loading error messages.
UX/UI
- Fix font issues.
- Fix SVG width in gene detail.
- Fix whitespace issues in BLAST queries.
- Fix default color inconsistency.
- Fix navbar issues.
Other
- Fix genome import.
- Fix genome sorting by species.
- Fix user creation.
- Fix pathway dropdown closing incorrectly.