usher-exploring

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gbanyan f33b048635 feat(01-04): add CLI entry point with setup and info commands

- Create click-based CLI with command group (--config, --verbose options)
- Add 'info' command displaying pipeline version, config hash, data source versions
- Add 'setup' command orchestrating full infrastructure flow:
  - Load config -> create store/provenance
  - Fetch gene universe (with checkpoint-restart)
  - Map Ensembl IDs to HGNC + UniProt
  - Validate mapping quality gates
  - Save to DuckDB with provenance sidecar
- Update pyproject.toml entry point to usher_pipeline.cli.main:cli
- Add .gitignore for data/, *.duckdb, build artifacts, provenance files

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

.planning

docs(01-02): complete gene ID mapping and validation plan

2026-02-11 16:35:57 +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(01-04): add CLI entry point with setup and info commands

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

tests

feat(01-02): create mapping validation gates with tests