gbanyan d57a5f2826 feat(04-03): add CLI score command with checkpoint-restart ...

- Created score_cmd.py following evidence_cmd.py pattern
- Orchestrates full scoring pipeline: known genes -> composite scores -> QC -> validation
- Options: --force, --skip-qc, --skip-validation for flexible iteration
- Registered score command in main CLI group
- Displays comprehensive summary with quality flag distribution

2026-02-11 20:52:37 +08:00

.planning

docs(04-02): complete QC and validation plan

2026-02-11 20:50:00 +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(04-03): add CLI score command with checkpoint-restart

2026-02-11 20:52:37 +08:00

tests

docs(03-04): complete subcellular localization evidence layer

2026-02-11 19:08:01 +08:00

.gitignore

feat(01-04): add CLI entry point with setup and info commands

2026-02-11 16:39:50 +08:00

pyproject.toml

feat(04-02): implement QC checks for scoring results

2026-02-11 20:46:57 +08:00

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