gbanyan
f33b048635
- 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
41 lines
327 B
Plaintext
41 lines
327 B
Plaintext
# Data files
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data/
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# DuckDB
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*.duckdb
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*.duckdb.wal
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# Python
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__pycache__/
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*.pyc
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*.pyo
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*.pyd
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.Python
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*.so
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*.egg
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*.egg-info/
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dist/
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build/
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.eggs/
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# Testing
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.pytest_cache/
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.coverage
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htmlcov/
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.tox/
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# IDE
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.vscode/
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.idea/
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*.swp
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*.swo
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*~
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# Provenance files (not in data/)
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/*.provenance.json
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# Virtual environment
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.venv/
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venv/
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env/
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