kemal
4c0ea5e04f
- signal/raw_xy.py: vectorised Infinium I/II raw X/Y and control assembly (plan §7.1) with a per-chip address-map cache; IN-027 coverage gate - core/schemas.py: Arrow schemas (loci, sample_intensity, controls), deterministic atomic Parquet writing - pipeline/ingest.py + CLI: discovery, sheet, IN-010 naming, overwrite check before any work, spawn-based workers, per-sample isolation, --resume by input hashes, run manifest, exit codes 0/3/4 - matches gtc2vcf raw X/Y and controls exactly on 18 GSA samples; outputs byte-identical across thread counts and layouts
66 lines
1.6 KiB
TOML
66 lines
1.6 KiB
TOML
[build-system]
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requires = ["hatchling>=1.24"]
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build-backend = "hatchling.build"
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[project]
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name = "simurg"
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description = "SimurgArray: open research toolkit for Illumina Infinium genotyping BeadChip data"
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readme = "README.md"
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license = { text = "MIT" }
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requires-python = ">=3.12"
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authors = [{ name = "Kemal Yaylali" }]
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dynamic = ["version"]
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dependencies = [
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"numpy>=1.26", # all numerics
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"typer>=0.12", # CLI
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"rich>=13", # progress / human-readable output
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"pyyaml>=6", # --config files
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"pyarrow>=15", # canonical columnar model and Parquet outputs (plan §5)
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]
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[project.optional-dependencies]
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dev = [
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"pytest>=8",
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"pytest-benchmark>=4",
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"hypothesis>=6.100",
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"ruff>=0.6",
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"mypy>=1.11",
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"types-PyYAML",
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]
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[project.scripts]
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simurg = "simurg.cli.main:app"
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[tool.hatch.version]
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path = "src/simurg/__init__.py"
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[tool.hatch.build.targets.wheel]
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packages = ["src/simurg"]
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[tool.pytest.ini_options]
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testpaths = ["tests"]
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addopts = "-q --strict-markers"
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markers = [
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"data: needs downloaded datasets under data/ (skipped when absent)",
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"oracle: compares against a reference implementation under refs/ (skipped when absent)",
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"slow: long-running test",
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]
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[tool.ruff]
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line-length = 120
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target-version = "py312"
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src = ["src", "tests"]
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[tool.ruff.lint]
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select = ["E", "F", "W", "I", "B", "UP", "N", "SIM", "RUF"]
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ignore = ["N802", "N806", "RUF001", "RUF002", "RUF003"]
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[tool.ruff.lint.per-file-ignores]
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"tests/**" = ["E501"]
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[tool.mypy]
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python_version = "3.12"
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strict = true
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files = ["src/simurg"]
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ignore_missing_imports = true
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