pyproject.toml

[build-system]
requires = ["flit_scm"]
build-backend = "flit_scm:buildapi"

[project]
name = "bioinf-maflib"
description = "Python package for processing and creating MAF files for the GDC"
authors = [
    {name = "Charles Czysz", email = "czysz@uchicago.edu"}
]

readme = "README.md"
requires-python = ">=3.8"
license = {file = "LICENSE"}
classifiers = [
    "License :: OSI Approved :: Apache Software License",
	"Programming Language :: Python :: 3",
	"Programming Language :: Python :: 3 :: Only"
]
dynamic = ["version"]
dependencies = [
    "click"
]

[project.optional-dependencies]
dev = [
    "black",
    "detect-secrets==1.4.0",
    "ruff",
    "isort",
    "mypy",
    "pre-commit>=2.9.0",
]

test = [
    "coverage[toml]",
    "pytest",
]

[project.urls]
homepage = "https://github.com/NCI-GDC/maf-lib"

[project.scripts]
"maflib" = "maflib.__main__:main"

[tool.setuptools_scm]
write_to = "maflib/_version.py"
local_scheme = "dirty-tag"
version_scheme = "python-simplified-semver"
fallback_version = "0"

[tool.coverage.run]
source = ["maflib"]
branch = true
parallel = true

[tool.flit.module]
name = "maflib"

[tool.flit.sdist]
include = ["maflib/_version.py"]
exclude = [
        ".*",
        "dev-requirements.*",
        "Dockerfile",
        "Jenkinsfile",
        "*travis.yml",
        "tox.ini",
]

[tool.black]
line-length = 88
skip-string-normalization = true
target-version = ['py38']

[tool.isort]
multi_line_output = 3
include_trailing_comma = true
force_grid_wrap = 0
use_parentheses=true
line_length = 88

[tool.mypy]
python_version = 3.8
disallow_untyped_defs = true
warn_return_any = true
warn_unused_configs = true

[tool.coverage.report]
show_missing = true

[tool.ruff]
# Enable pycodestyle (`E`) and Pyflakes (`F`) codes by default.
select = ["E", "F"]
ignore = ["E501"]

# Allow autofix for all enabled rules (when `--fix`) is provided.
fixable = ["A", "B", "C", "D", "E", "F"]
unfixable = []

# Exclude a variety of commonly ignored directories.
exclude = [
    ".bzr",
    ".direnv",
    ".eggs",
    ".git",
    ".mypy_cache",
    ".pytype",
    ".ruff_cache",
    ".tox",
    ".venv",
    "__pypackages__",
    "_build",
    "build",
    "dist",
    "node_modules",
    "venv",
]

# Same as Black.
line-length = 88

# Allow unused variables when underscore-prefixed.
dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"

# Assume Python 3.10.
target-version = "py38"

[tool.ruff.mccabe]
# Unlike Flake8, default to a complexity level of 10.
max-complexity = 10

[tool.ruff.per-file-ignores]
"__init__.py" = ["E402"]