https://github.com/cbg-ethz/v-pipe-scout - Release v0.4.2-beta

🚀 Features

• Configurable Streamlit Port: Added STREAMLIT_PORT environment variable for flexible deployment
• Python 3.13 Upgrade: ~4% performance improvement, latest features, and enhanced debugging

🐛 Fixes

• Abundance Estimator: Fixed mutation sorting and variant signature matrix bugs

📦 Changes

• Updated Docker Compose for dynamic port mapping
• Upgraded dependencies (Streamlit 1.48.0, Celery 5.5.3)
• Added comprehensive test coverage for variant processing

- Python
Published by gordonkoehn 6 months ago

https://github.com/cbg-ethz/v-pipe-scout - v0.4.1-beta

What's Changed

• feat: continuous deployment by @gordonkoehn in https://github.com/cbg-ethz/v-pipe-scout/pull/142
• feat: region state and defaults // docs: CI/CD note readme by @gordonkoehn in https://github.com/cbg-ethz/v-pipe-scout/pull/143

Full Changelog: https://github.com/cbg-ethz/v-pipe-scout/compare/v0.4.0-beta...v0.4.1-beta

- Python
Published by gordonkoehn 6 months ago

https://github.com/cbg-ethz/v-pipe-scout - Release v0.4.0-beta

🚀 New Features

🔍 Region Explorer

• New "Region Explorer" page for exploring mutations in specific genomic regions or custom mutation sets
• Primer design support: Perfect for primer design and redesign workflows
• Flexible analysis modes: Support for both custom mutation sets and genomic range-based analysis
• Enhanced data integrity: Improved duplicate detection and removal in API responses

🔗 Complete URL State Management

• Full URL sharing support across all analysis pages
• Persistent user settings: Date ranges, locations, frequency thresholds, and display options saved to URLs
• Smart variant handling: Curated variants automatically saved with clear user notifications

🔧 Improvements

📊 Enhanced Components

• Improved Mutation Plot Component: Better integration with URL state management
• Standardized data handling: Consistent mutation type processing across the application
• Better error handling: More robust API response processing

🎨 User Experience

• Clear user guidance: Informational messages explaining URL sharing limitations
• Improved navigation: Better page organization and user flow

🐛 Bug Fixes

• Fixed duplicate heading in Region Explorer page
• Resolved abundance async issues in abundance estimator
• Fixed missing async handling in various components
• Corrected wording and UI inconsistencies

📈 Technical Updates

Dependencies

• Streamlit upgraded: 1.47.0 → 1.49.0 with comprehensive compatibility testing
• Performance improvements: Latest bug fixes and optimizations from Streamlit

Testing

• Comprehensive API compatibility testing for all Streamlit patterns
• Verified backward compatibility with zero breaking changes

📋 Files Changed

• New files: app/subpages/region.py, app/utils/url_state.py, docs/URL_SHARING.md
• Enhanced files: Multiple subpages with URL state integration

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Full Changelog: v0.3.0-beta...v0.4.0-beta

- Python
Published by gordonkoehn 6 months ago

https://github.com/cbg-ethz/v-pipe-scout - v0.3.0-beta

Initial public release.

:loudspeaker: Query Wastewater on the Read Level Interactively Online with V-Pipe Scout – Now at https://wasap.genspectrum.org/

V-Pipe Scout, a proof-of-concept tool, enables rapid querying of wastewater data at the read level, currently offering one month of COVID-19 data for experimental research.

Are known resistance mutations present? Is this variant present? Explore immediately.

Developed by the Computational Evolution and Computational Biology Groups, it’s the first step toward a Wastewater Analysis and Sharing Platform (W-ASAP), built on the Loculus software, and its fast query engine SILO, both developed by the Computational Evolution Group.

Primarily an internal tool, select visualisations shall be integrated into GenSpectrum’s Wastewater section for broader accessibility. We invite you to explore V-Pipe Scout and share your feedback to help shape its development.

- Python
Published by gordonkoehn 7 months ago