pyproject.toml

[project]
name = "kraken-db-builder"
version = "0.1.1"
description = "CLI tool to build any kraken2 database with single command"
readme = "README.md"
license = {file = "LICENSE.txt"}
maintainers = [{name = "ChillarAnand", email = "chillar@avilpage.com"}]
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Developers",
    "License :: OSI Approved :: MIT License",
    "Operating System :: OS Independent",
    "Programming Language :: Python",
    "Typing :: Typed",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Utilities",
]
requires-python = ">=3.8"
dependencies = [
    "ncbi-genome-download",
    "click",
]

[project.urls]
Documentation = "https://avilpage.com/kdb.html"
Source = "https://github.com/avilpage/kraken-db-builder"

[build-system]
requires = ["flit_core<4"]
build-backend = "flit_core.buildapi"

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

[tool.flit.sdist]
include = [
    "requirements/",
    "tests/",
]
exclude = [
    "docs/_build/",
]

[tool.pytest.ini_options]
testpaths = ["tests"]
filterwarnings = [
    "error",
]

[tool.coverage.run]
branch = true
source = ["click", "tests"]

[tool.coverage.paths]
source = ["src", "*/site-packages"]

[tool.mypy]
python_version = "3.8"
files = ["src/click", "tests/typing"]
show_error_codes = true
pretty = true
strict = true

ignore_missing_imports = true

[tool.pyright]
pythonVersion = "3.8"
include = ["src/click", "tests/typing"]
typeCheckingMode = "basic"

[tool.ruff]
extend-exclude = ["examples/"]
src = ["src"]
fix = true
show-fixes = true
output-format = "full"

[tool.ruff.lint]
select = [
    "B",  # flake8-bugbear
    "E",  # pycodestyle error
    "F",  # pyflakes
    "I",  # isort
    "UP",  # pyupgrade
    "W",  # pycodestyle warning
]
ignore-init-module-imports = true

[tool.ruff.lint.isort]
force-single-line = true
order-by-type = false

[project.scripts]
kdb = "kdb:main"
kraken-db-builder = "kdb:main"