pyproject.toml

[build-system]
requires = ["setuptools>=75.8.0", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "cubi-tk"
description = "Add your description here"
readme = "README.md"
requires-python = ">=3.12"
dynamic = ["version"]
dependencies = [
    "argcomplete>=3.5.3",
    "attrs>=24.3.0",
    "biomedsheets",
    "cattrs>=24.1.2",
    "cookiecutter==2.3.1",
    "cubi-isa-templates==0.1.1",
    "hpo-similarity>=0.5.3",
    "icdiff>=2.0.7",
    "logzero>=1.7.0",
    "pandas>=2.2.3",
    "python-irodsclient==1.1.8",
    "pyyaml>=6.0.2",
    "requests>=2.32.3",
    "retrying>=1.3.4",
    "simplejson>=3.19.3",
    "termcolor>=2.5.0",
    "toml>=0.10.2",
    "toolz>=1.0.0",
    "toposort>=1.10",
    "tqdm>=4.67.1",
    "varfish-cli>=0.6.2,<0.7.0",
    "vcfpy >=0.13.8",
    "altamisa @ git+https://github.com/bihealth/altamisa.git@817dc491ff819e4c80686082bf3e5f602f1ac14c",
    "biomedsheets @ git+https://github.com/bihealth/biomedsheets@4e0a8484850c39d1511036c3fe29ec0b4f9271f8",
    "sodar-cli @ git+https://github.com/bihealth/sodar-cli@a62505ff9b1365f150bce54c9b2b5e638f245f86",
]

[project.license]
file = "LICENSE"

[project.scripts]
cubi-tk = "cubi_tk.__main__:main"

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

[tool.pytest.ini_options]
addopts = [
    "--import-mode=importlib",
]
pythonpath = [
    ".", "tests"
]

[project.optional-dependencies]
snappy = [
    "snappy-pipeline @ git+https://github.com/bihealth/snappy-pipeline@5d11f311357e75516ba2d7045cc0c1bd61201e14",
]
all = ["cubi-tk[snappy]"]

[dependency-groups]
dev = [
    "factory-boy>=3.2.0",
    "pyfakefs>=3.7.1",
    "pytest>=4.0",
    "pytest-cache>=1.0",
    "pytest-cov>=2.4.0",
    "pytest-mock>=2.0.0",
    "pytest-runner>=2.11",
    "requests-mock>=1.7.0",
    "ruff>=0.9.0",
    "setuptools>=75.8.0",
    "tox>=4.23",
]
docs = [
    "sphinx>=1.7.0",
    "sphinx-rtd-theme>=0.4.3",
    "sphinx-argparse>=0.2.5",
    "recommonmark>=0.6.0",
]

[tool.ruff]
# Exclude a variety of commonly ignored directories.
exclude = [
    ".bzr",
    ".direnv",
    ".eggs",
    ".git",
    ".git-rewrite",
    ".hg",
    ".ipynb_checkpoints",
    ".mypy_cache",
    ".nox",
    ".pants.d",
    ".pyenv",
    ".pytest_cache",
    ".pytype",
    ".ruff_cache",
    ".svn",
    ".tox",
    ".venv",
    ".vscode",
    "__pypackages__",
    "_build",
    "buck-out",
    "build",
    "dist",
    "node_modules",
    "site-packages",
    "venv",
]
line-length = 100
indent-width = 4

[tool.ruff.lint]
ignore = ["E203", "E266", "E501", "E741"]
select = ["B", "C", "E", "F", "W"]