pyproject.toml

[project]
name = "pyllelic"
authors = [{ name = "Andrew J. Bonham", email = "bonham@gmail.com" }]
readme = "README.md"
description = "Analysis of allele-specific methylation in bisulfite DNA sequencing."
license = { file = "LICENSE" }
requires-python = ">=3.8"
classifiers = [
        "Programming Language :: Python :: 3",
        "Programming Language :: Python :: 3.8",
        "Programming Language :: Python :: 3.9",
        "Programming Language :: Python :: 3.10",
        "Programming Language :: Python :: 3 :: Only",
        "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
        "Operating System :: OS Independent",
]
dependencies = [
        "pandas",
        "numpy",
        "scipy",
        "plotly",
        "matplotlib",
        "xlsxwriter",
        "xlrd",
        "openpyxl",
        "tqdm",
        "pysam",
        "biopython",
        "seaborn",
        "requests",
]
keywords = ["genomics", "methylation", "DNA sequencing"]
dynamic = ["version"]

[project.urls]
Homepage = "https://github.com/Paradoxdruid/pyllelic"

[project.optional-dependencies]
dev = [
        "black",
        "pytest",
        "pytest-mock",
        "mypy",
        "types-requests",
        "ruff",
        "requests-mock",
        "pre-commit",
]

[tool.setuptools]
packages = ["pyllelic"]

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

[build-system]
requires = ["setuptools", "setuptools-scm"]
build-backend = "setuptools.build_meta"

[tool.pytest.ini_options]
filterwarnings = ["ignore::DeprecationWarning"]

[tool.mypy]
ignore_missing_imports = true
strict = true
files = "pyllelic/*.py"

[tool.isort]
profile = "black"

[tool.ruff]
select = ["E", "F", "B", "W", "I", "C4", "PIE", "PYI"]
ignore = ["B905"]