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f33b048635
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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
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2026-02-11 16:39:50 +08:00 |
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