- Docker:
- Explicitly install pixi environments (digger, pipeline, webbackend) during build to prevent runtime network/DNS failures.
- Optimize pnpm config (copy method) to fix EAGAIN errors.
- Backend:
- Refactor ZIP bundling: use flat semantic directories (1_Toxin_Mining, etc.).
- Fix "nested zip" issue by cleaning existing archives before bundling.
- Exclude raw 'context' directory from final download.
- Frontend:
- Update TutorialView documentation to match new result structure.
- Improve TaskMonitor progress bar precision (1 decimal place).
- Update i18n (en/zh) for new file descriptions.
Co-Authored-By: Claude <noreply@anthropic.com>
- Backend: Refactored tasks.py to directly invoke run_single_fna_pipeline.py for consistency.
- Backend: Changed output format to ZIP and added auto-cleanup of intermediate files.
- Backend: Fixed language parameter passing in API and tasks.
- Frontend: Removed CRISPR Fusion UI elements from Submit and Monitor views.
- Frontend: Implemented simulated progress bar for better UX.
- Frontend: Restored One-click load button and added result file structure documentation.
- Docker: Fixed critical Restarting loop by removing incorrect image directive in docker-compose.yml.
- Docker: Optimized Dockerfile to correct .pixi environment path issues and prevent accidental deletion of frontend assets.
- Updated AGENTS.md and README.md to reflect:
- Removal of motia-backend
- Moving bttoxin_digger_v5_repro to tools/reproduction/
- Added crispr_cas to structure
- Add property-based tests for PixiRunner
- Add HAN055.fna test data file
- Update README with pixi installation and usage guide
- Update .gitignore for pixi and test artifacts
- Update CLI to remove Docker-related arguments
