usher-exploring

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gbanyan bcd3c4ffbe feat(03-05): add animal model DuckDB loader, CLI, and comprehensive tests

- load.py: DuckDB persistence with provenance tracking, ortholog confidence distribution stats
- CLI animal-models command: checkpoint-restart pattern, top scoring genes display
- 10 unit tests: ortholog confidence scoring, keyword filtering, multi-organism bonus, NULL preservation
- 4 integration tests: full pipeline, checkpoint-restart, provenance tracking, empty phenotype handling
- All tests pass (14/14): validates fetch->transform->load->CLI flow
- Fixed polars deprecations: str.join replaces str.concat, pl.len replaces pl.count

2026-02-11 19:06:49 +08:00

.planning

docs(03-01): complete annotation completeness plan

2026-02-11 19:05:56 +08:00

config

feat(01-01): create Python package scaffold with config system

2026-02-11 16:24:35 +08:00

src/usher_pipeline

feat(03-05): add animal model DuckDB loader, CLI, and comprehensive tests

2026-02-11 19:06:49 +08:00

tests

feat(03-05): add animal model DuckDB loader, CLI, and comprehensive tests