pyproject.toml

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

[tool.setuptools.packages]
find = {}

[tool.setuptools_scm]
write_to = "bigwig_loader/_version.py"
version_scheme = "post-release"
fallback_version = "0.0.0"

[project]
name = "bigwig_loader"
authors = [
    {name = "Joren Retel", email = "joren.retel@pfizer.com"},
]
description = "Machine Learning Data Loader for Collections of BigWig Files"
readme = "README.md"
requires-python = ">=3.10"
keywords = ["epigenetics", "bigwig", "fasta"]
license = {text = "Apache-2.0"}
classifiers = [
    "Development Status :: 3 - Alpha",
    "Intended Audience :: Science/Research",
    "Programming Language :: Python",
    "Programming Language :: Python :: 3 :: Only",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Topic :: Scientific/Engineering",
    "Topic :: Utilities"
]
dependencies = [
    "numpy",
    "cupy",
    "cython",
    "pandas",
    "ncls",
    "pyfaidx",
    "pydantic",
    "pydantic-settings",
    "python-dotenv",
    "universal_pathlib",
    "natsort",
]
dynamic = ["version"]

[project.urls]
homepage = "https://github.com/pfizer-opensource/bigwig-loader"

[project.optional-dependencies]
test = ["mypy", "pytest", "pyBigWig"]
dev = ["bigwig_loader[test]", "black", "isort", "bandit", "pip-tools", "pre-commit"]

[tool.pytest.ini_options]
log_cli = false
log_cli_level = "DEBUG"
log_cli_format = "%(asctime)s [%(levelname)8s] %(message)s (%(filename)s:%(lineno)s)"
log_cli_date_format = "%Y-%m-%d %H:%M:%S"

[tool.mypy]
python_version = "3.10"
check_untyped_defs = true
disallow_any_generics = true
disallow_incomplete_defs = true
disallow_untyped_defs = true
namespace_packages = true
no_implicit_optional = true
warn_redundant_casts = true
warn_return_any = true
warn_unused_configs = true
warn_unused_ignores = false
exclude = "tests|examples|benchmark"

[tool.isort]
profile = "black"
py_version = "38"
force_single_line = true

[[tool.mypy.overrides]]
module = "cupy.*,zarr.*,pandas.*,numcodecs.*,fsspec.*,pyfaidx.*,ncls.*,bigwig_loader.merge_intervals.*,bigwig_loader.subtract_intervals.*,torch.*,kvikio.*"
ignore_missing_imports = true

[tool.bandit]
skips = ["B603", "B310", "B607", "B404"]
exclude = "./tests/test_*.py"

[tool.bandit.assert_used]
skips = ["./tests/test_*.py"]

[tool.codespell]
ignore-words-list = " "