MolDef-spec-python/pyproject.toml at main · InformaticsGenomicMedicine/MolDef-spec-python · GitHub

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[project]
name = "moldef.spec"
version = "0.3.0"
description = "Python implementation of the HL7 FHIR MolecularDefinition resource with support for associated profiles."
readme = "README.md"
authors = [
    {name = "Salem Bajjali"},
    {name = "Robert R. Freimuth"},
]

license = {file = "LICENSE"}
requires-python = ">=3.11"

keywords = [
    "FHIR",
    "HL7",
    "MolecularDefinition",
    "genomics",
    "variation",
    "representation",
]

classifiers = [
    "Intended Audience :: Developers",
    "Intended Audience :: Healthcare Industry",
    "Intended Audience :: Science/Research",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "License :: OSI Approved :: Apache Software License",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
]

dependencies = [
    "fhir-core==1.1.4",
    "fhir-resources==8.0.0",
    "ipykernel==6.28.0",
    ]

[project.optional-dependencies]
dev = [
    "pytest==7.4.4",
    "deepdiff==8.6.1",
    "ruff==0.8.3"
]

[build-system]
requires = ["setuptools>=65.3", "setuptools_scm>=8"]
build-backend = "setuptools.build_meta"

[tool.setuptools.packages.find]
where = ["src"]

[tool.ruff]
src = ["src"]
exclude = ["notebooks", "data", "edits"]

[tool.ruff.lint]

select = [
    "F",  # https://docs.astral.sh/ruff/rules/#pyflakes-f
    "E", "W",  # https://docs.astral.sh/ruff/rules/#pycodestyle-e-w
    "I",  # https://docs.astral.sh/ruff/rules/#isort-i
    "B",  # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b
    "UP",  # https://docs.astral.sh/ruff/rules/#pyupgrade-up
    "SIM",  # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
    "ARG",  # https://docs.astral.sh/ruff/rules/#flake8-unused-arguments-arg
    "S",  # https://docs.astral.sh/ruff/rules/#flake8-bandit-s
   ]

ignore = ["E501"] # Ruff format already handles long lines
fixable = ["ALL"]

[tool.ruff.format]
quote-style = "double"  # Enforce double quotes
docstring-code-format = true  # Format code inside docstrings