[build-system]
requires = ["setuptools>=61.0", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "usher-pipeline"
version = "0.1.0"
description = "Reproducible pipeline for discovering under-studied cilia/Usher candidate genes"
requires-python = ">=3.11"
authors = [
    {name = "Research Team"}
]
readme = "README.md"
license = {text = "MIT"}
classifiers = [
    "Development Status :: 3 - Alpha",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]

dependencies = [
    "mygene>=3.2.0",
    "requests>=2.31.0",
    "requests-cache>=1.1.0",
    "tenacity>=8.2.0",
    "pydantic>=2.0",
    "pydantic-yaml>=1.2.0",
    "duckdb>=0.9.0",
    "click>=8.1.0",
    "polars>=0.19.0",
    "pyarrow>=14.0.0",
    "pyyaml>=6.0",
    "httpx>=0.28",
    "structlog>=25.0",
    "biopython>=1.84",
]

[project.optional-dependencies]
dev = [
    "pytest>=7.4.0",
    "pytest-cov>=4.1.0",
]
expression = [
    "cellxgene-census>=1.19",
]

[project.scripts]
usher-pipeline = "usher_pipeline.cli.main:cli"

[tool.setuptools]
packages = ["usher_pipeline"]
package-dir = {"" = "src"}

[tool.pytest.ini_options]
testpaths = ["tests"]
python_files = ["test_*.py"]
python_functions = ["test_*"]
addopts = "-v --strict-markers"