dcd_mapping/pyproject.toml at main · VariantEffect/dcd_mapping · GitHub

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[project]
name = "dcd-mapping"
description = "Map MaveDB scoresets to VRS objects"
authors = [
    {name = "Alex Handler Wagner", email = "Alex.Wagner@nationwidechildrens.org"},
    {name = "Jeremy Arbesfeld", email = "Jeremy.Arbesfeld@nationwidechildrens.org"},
    {name = "Samriddhi Singh", email = "todo@todo.org"},
    {name = "James Stevenson", email = "James.Stevenson@nationwidechildrens.org"},
]
readme = "README.md"
version = "0.0.1"
license = { file = "LICENSE" }
classifiers = [
    "Development Status :: 3 - Alpha",
    "Framework :: Pydantic",
    "Framework :: Pydantic :: 2",
    "Programming Language :: Python",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3 :: Only",
    "Programming Language :: Python :: 3.8",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Intended Audience :: Science/Research",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]
requires-python = ">=3.11"
dependencies = [
    "requests",
    "biopython",
    "tqdm",
    "click",
    "cool-seq-tool>=0.4.0.dev1",
    "gene-normalizer>=0.3.0-dev1",
    "pydantic>=2",
    "python-dotenv",
]

[project.scripts]
dcd-map = "dcd_mapping.cli:cli"

[project.optional-dependencies]
tests = [
    "pytest",
    "pytest-mock",
    "pytest-cov",
    "pytest-asyncio"
]
dev = [
    "ruff>=0.1.14",
    "pre-commit"
]

[project.urls]
Homepage = "https://www.varianteffect.org/"
Documentation = "https://github.com/ave-dcd/dcd_mapping/README.md"
Source = "https://github.com/ave-dcd/dcd_mapping"


[build-system]
requires = ["setuptools"]
build-backend = "setuptools.build_meta"

[tool.pytest.ini_options]
addopts = "--cov=src --cov-report term-missing"
testpaths = ["tests"]
asyncio_mode = "auto"


[tool.coverage.run]
branch = true

[tool.ruff]
src = ["src"]
exclude = ["misc/*"]
# pycodestyle (E, W)
# Pyflakes (F)
# flake8-annotations (ANN)
# pydocstyle (D)
# pep8-naming (N)
# isort (I)
select = ["E", "W", "F", "ANN", "D", "N", "I", "T201", "T100"]
fixable = ["I", "F401", "T201", "T100"]
include = ["pyproject.toml", "tests/**/*.py", "src/**/*.py"]

# ANN101 - missing-type-self
# ANN003 - missing-type-kwargs
# D203 - one-blank-line-before-class
# D205 - blank-line-after-summary
# D206 - indent-with-spaces*
# D213 - multi-line-summary-second-line
# D300 - triple-single-quotes*
# D400 - ends-in-period
# D415 - ends-in-punctuation
# E111 - indentation-with-invalid-multiple*
# E114 - indentation-with-invalid-multiple-comment*
# E117 - over-indented*
# E501 - line-too-long*
# W191 - tab-indentation*
# *ignored for compatibility with formatter
ignore = [
    "ANN101", "ANN003",
    "D203", "D205", "D206", "D213", "D300", "D400", "D415",
    "E111", "E114", "E117", "E501",
    "W191"
]

[tool.ruff.per-file-ignores]
# ANN001 - missing-type-function-argument
# ANN2 - missing-return-type
# ANN102 - missing-type-cls
"tests/*" = ["ANN001", "ANN102", "ANN2"]