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pyproject.toml
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[project]
name = "therapy-normalizer"
authors = [
{name = "Alex Wagner"},
{name = "Kori Kuzma"},
{name = "James Stevenson"}
]
readme = "README.md"
classifiers = [
"Development Status :: 3 - Alpha",
"Framework :: FastAPI",
"Framework :: Pydantic",
"Framework :: Pydantic :: 2",
"Intended Audience :: Science/Research",
"Intended Audience :: Developers",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"License :: OSI Approved :: MIT License",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
]
requires-python = ">=3.8"
description = "VICC normalization routines for therapeutics"
license = {file = "LICENSE"}
dependencies = [
"pydantic==2.*",
"fastapi",
"uvicorn",
"click",
"boto3",
"ga4gh.vrs~=2.0.0a1",
]
dynamic = ["version"]
[project.optional-dependencies]
etl = ["disease-normalizer~=0.4.0.dev0", "owlready2", "rdflib", "wikibaseintegrator>=0.12.0", "chembl-downloader", "bioversions>=0.4.3"]
test = ["pytest", "pytest-cov"]
dev = ["pre-commit", "ruff>=0.1.2", "lxml", "xmlformatter", "mypy", "types-requests", "types-pyyaml"]
[project.urls]
Homepage = "https://github.com/cancervariants/therapy-normalization"
Documentation = "https://github.com/cancervariants/therapy-normalization"
Changelog = "https://github.com/cancervariants/therapy-normalization/releases"
Source = "https://github.com/cancervariants/therapy-normalization"
"Bug Tracker" = "https://github.com/cancervariants/therapy-normalization/issues"
[build-system]
requires = ["setuptools>=61.0"]
build-backend = "setuptools.build_meta"
[tool.setuptools.dynamic]
version = {attr = "therapy.version.__version__"}
[tool.setuptools.packages.find]
where = ["src"]
[tool.setuptools.package-data]
"therapy.etl" = ["*.csv"]
[tool.pytest.ini_options]
addopts = "--cov=src --cov-report term-missing"
testpaths = ["tests"]
[tool.coverage.run]
branch = true
[tool.mypy]
plugins = "pydantic.mypy"
ignore_missing_imports = true
[tool.ruff]
src = ["src"]
# pycodestyle (E, W)
# Pyflakes (F)
# flake8-annotations (ANN)
# pydocstyle (D)
# pep8-naming (N)
# isort (I)
select = ["E", "W", "F", "ANN", "D", "N", "I"]
fixable = ["I", "F401"]
# D203 - one-blank-line-before-class
# D205 - blank-line-after-summary
# D206 - indent-with-spaces*
# D213 - multi-line-summary-second-line
# D400 - ends-in-period
# D415 - ends-in-punctuation
# ANN101 - missing-type-self
# ANN003 - missing-type-kwargs
# E501 - line-too-long
# W191 - tab-indentation*
# *ignored for compatibility with formatter
ignore = ["D203", "D205", "D206", "D213", "D400", "D415", "ANN101", "ANN003", "E501", "Q", "W191"]
[tool.ruff.per-file-ignores]
# ANN001 - missing-type-function-argument
# ANN2 - missing-return-type
# ANN201 - Missing type annotation
# ANN102 - missing-type-cls
# D103 - Missing docstring in public function
# F821 - undefined-name
# F401 - unused-import
# I001 - Import block unsorted or unformatted
# N805 - invalid-first-argument-name-for-method
"tests/*" = ["ANN001", "ANN102", "ANN2"]
"setup.py" = ["F821"]
"*__init__.py" = ["F401"]
"therapy/schemas.py" = ["ANN001", "ANN201", "N805"]
"docs/source/conf.py" = ["D100", "I001", "D103", "ANN201", "ANN001"]