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
56 lines
1.3 KiB
TOML
56 lines
1.3 KiB
TOML
[build-system]
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requires = ["setuptools>=61.0", "wheel"]
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build-backend = "setuptools.build_meta"
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[project]
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name = "usher-pipeline"
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version = "0.1.0"
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description = "Reproducible pipeline for discovering under-studied cilia/Usher candidate genes"
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requires-python = ">=3.11"
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authors = [
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{name = "Research Team"}
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]
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readme = "README.md"
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license = {text = "MIT"}
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classifiers = [
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"Development Status :: 3 - Alpha",
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"Intended Audience :: Science/Research",
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"License :: OSI Approved :: MIT License",
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"Programming Language :: Python :: 3.11",
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"Programming Language :: Python :: 3.12",
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"Topic :: Scientific/Engineering :: Bio-Informatics",
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]
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dependencies = [
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"mygene>=3.2.0",
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"requests>=2.31.0",
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"requests-cache>=1.1.0",
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"tenacity>=8.2.0",
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"pydantic>=2.0",
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"pydantic-yaml>=1.2.0",
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"duckdb>=0.9.0",
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"click>=8.1.0",
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"polars>=0.19.0",
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"pyarrow>=14.0.0",
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"pyyaml>=6.0",
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]
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[project.optional-dependencies]
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dev = [
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"pytest>=7.4.0",
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"pytest-cov>=4.1.0",
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]
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[project.scripts]
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usher-pipeline = "usher_pipeline.cli.main:cli"
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[tool.setuptools]
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packages = ["usher_pipeline"]
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package-dir = {"" = "src"}
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[tool.pytest.ini_options]
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testpaths = ["tests"]
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python_files = ["test_*.py"]
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python_functions = ["test_*"]
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addopts = "-v --strict-markers"
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