qimu/pyproject.toml at main · quadram-institute-bioscience/qimu · GitHub

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[build-system]
requires = ["setuptools>=65.0", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "qimu"
dynamic = ["version"]
description = "A modern Python CLI toolset for bioinformatics"
readme = "README.md"
requires-python = ">=3.10"
license = {text = "MIT"}
authors = [
    {name = "Your Name", email = "your.email@example.com"}
]
classifiers = [
    "Development Status :: 3 - Alpha",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]
dependencies = [
    "rich>=13.0.0",
    "rich-click>=1.7.0",
    # Data analysis packages
    "numpy>=1.24.0",
    "pandas>=2.0.0",
    "matplotlib>=3.7.0",
    "seaborn>=0.12.0",
    "scikit-learn>=1.3.0",
    "plotly>=5.14.0",
    # Bioinformatics packages
    "pyfastx>=2.0.0",
    "newick>=1.10",
    "pysam>=0.21.0",
    "pyvcf3>=1.0.3",
]

[project.optional-dependencies]
dev = [
    "pytest>=7.4.0",
    "pytest-cov>=4.1.0",
    "ruff>=0.1.0",
    "black>=23.0.0",
]

[project.scripts]
qimu = "qimu.cli:main"

[tool.setuptools.dynamic]
version = {attr = "qimu.__version__"}

[tool.setuptools.packages.find]
where = ["."]
include = ["qimu*"]

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

[tool.ruff]
line-length = 100
target-version = "py310"

[tool.ruff.lint]
select = [
    "E",   # pycodestyle errors
    "W",   # pycodestyle warnings
    "F",   # pyflakes
    "I",   # isort
    "B",   # flake8-bugbear
    "C4",  # flake8-comprehensions
    "UP",  # pyupgrade
]
ignore = [
    "E501",  # line too long (handled by black)
]

[tool.ruff.lint.per-file-ignores]
"__init__.py" = ["F401"]  # unused imports in __init__.py
"qimu/cli.py" = ["E402"]  # module level imports not at top (needed to avoid circular imports)

[tool.black]
line-length = 100
target-version = ['py310', 'py311', 'py312']
include = '\.pyi?$'