Orographer/pyproject.toml at main · PacificBiosciences/Orographer · GitHub

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[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[project]
name = "orographer"
version = "0.1.0"
description = "command line tool for visualizing split alignments from BAM files"
readme = "README.md"
requires-python = ">=3.10"
license = { text = "Proprietary" }
authors = [
    { name = "Jonathan Belyeu", email = "jbelyeu@pacificbiosciences.com" }
]
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "License :: Other/Proprietary License",
]
dependencies = [
    "bokeh>=3.0.0",
    "intervaltree>=3.1.0",
    "pysam>=0.23.0",
]

[project.optional-dependencies]
# End-to-end shell script (tests/scripts/run_end_to_end_tests.sh): CPython venv + pytest +
# ruff (lint/format gate) + tests/scripts/compare_files.py (pysam + skimage for HTML SSIM).
e2e = [
    "pytest>=8.3,<9",
    "ruff>=0.8",
    "scikit-image>=0.22",
]
dev = [
    "pytest==8.3.5",
    "pytest-cov",
    "black",
    "isort",
    "mypy",
    "ruff",
    "pre-commit",
]

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

[tool.hatch.build.targets.wheel]
packages = ["orographer"]

[tool.hatch.build.targets.sdist]
include = [
    "orographer",
    "LICENSE.md",
    "README.md",
]

[tool.hatch.envs.default]
dependencies = [
    "pytest",
    "pytest-cov",
]

[tool.hatch.envs.default.scripts]
test = "pytest {args:tests}"
test-cov = "pytest --cov-report=term-missing --cov-config=pyproject.toml --cov=orographer {args:tests}"
lint = [
    "ruff check .",
    "ruff format --check .",
    "black --check .",
    "isort --check-only .",
    "mypy .",
]
format = [
    "ruff check --fix .",
    "ruff format .",
    "black .",
    "isort .",
]

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

[tool.isort]
profile = "black"
multi_line_output = 3

[tool.mypy]
python_version = "3.10"
strict = true
ignore_missing_imports = true

[tool.ruff]
line-length = 100
target-version = "py311"

[tool.ruff.lint]
select = ["E", "F", "I", "UP", "B", "C4", "SIM", "RUF"]
ignore = []

[tool.ruff.format]
quote-style = "double"
indent-style = "space"

[tool.pytest.ini_options]
testpaths = ["tests"]
python_files = ["test_*.py"]
addopts = "-ra -q"
markers = [
    "slow: slow integration tests (e.g., deploy smoke tests)",
]