looper/pyproject.toml at master · pepkit/looper · GitHub

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[project]
name = "looper"
version = "2.1.0"
description = "A pipeline submission engine that parses sample inputs and submits pipelines for each sample."
readme = "README.md"
license = "BSD-2-Clause"
requires-python = ">=3.10"
authors = [
    { name = "Nathan Sheffield" },
    { name = "Vince Reuter" },
    { name = "Michal Stolarczyk" },
    { name = "Johanna Klughammer" },
    { name = "Andre Rendeiro" },
    { name = "Donald Campbell" },
]
keywords = ["bioinformatics", "sequencing", "ngs"]
classifiers = [
    "Development Status :: 4 - Beta",
    "License :: OSI Approved :: BSD License",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Programming Language :: Python :: 3.14",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]
dependencies = [
    "colorama>=0.3.9",
    "eido>=0.2.4",
    "jinja2",
    "logmuse>=0.2.0",
    "pandas>=2.0.2",
    "pephubclient>=0.4.0",
    "pipestat>=0.12.0a1",
    "peppy>=0.40.6",
    "pyyaml>=3.12",
    "rich>=9.10.0",
    "ubiquerg>=0.8.1",
    "yacman @ git+https://github.com/databio/yacman.git@dev",  # TODO: revert to yacman>=0.9.5 after release
    "pydantic-settings>=2.0.0",
    "psutil",
]

[project.urls]
Homepage = "https://github.com/pepkit/looper"

[project.scripts]
looper = "looper.cli_pydantic:main_cli"
divvy = "looper.__main__:divvy_main"

[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[tool.hatch.metadata]
allow-direct-references = true

[project.optional-dependencies]
api = [
    "fastapi>=0.100.0",
    "uvicorn>=0.22.0",
]
test = [
    "hypothesis>=6.84.3",
    "mock",
    "pytest",
    "pytest-cov",
    "pytest-remotedata",
    "GitPython",
    "psutil",
]

[tool.pytest.ini_options]
addopts = "-rfE"
testpaths = ["tests/unit", "tests/divvytests"]  # Fast tests only by default
# Integration tests: RUN_INTEGRATION_TESTS=true pytest tests/integration
python_files = ["test_*.py"]
python_classes = ["Test*", "*Test", "*Tests", "*Tester"]
python_functions = ["test_*"]

[tool.ruff]
line-length = 88

[tool.ruff.lint]
select = ["E", "F", "I"]
ignore = ["F403", "F405", "E501"]

[tool.ruff.lint.per-file-ignores]
"looper/__init__.py" = ["E402", "F401"]
"looper/looper.py" = ["E402"]
"looper/processed_project.py" = ["E402", "F821"]
"tests/**" = ["F841", "E712", "E722"]

[tool.ruff.lint.isort]
known-first-party = ["looper"]