FHIR-PYrate/pyproject.toml at main · UMEssen/FHIR-PYrate · GitHub

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[build-system]
build-backend = "setuptools.build_meta"
requires = [ "setuptools>=80", "wheel" ]

[project]
name = "fhir-pyrate"
version = "0.2.5"
description = """\
  FHIR-PYrate is a package that provides a high-level API to query FHIR Servers for bundles of resources and return \
  the structured information as pandas DataFrames. It can also be used to filter resources using RegEx and SpaCy and \
  download DICOM studies and series.\
  """
readme = "README.md"
keywords = [ "data-science", "fhir", "fhirpath", "healthcare", "python" ]
license-files = [ "LICENSE" ]
authors = [
  { name = "Giulia Baldini", email = "giulia.baldini@uk-essen.de" },
  { name = "Rene Hosch", email = "rene.hosch@uk-essen.de" },
]
requires-python = ">=3.10"
classifiers = [
  "Programming Language :: Python :: 3 :: Only",
  "Programming Language :: Python :: 3.10",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
  "Programming Language :: Python :: 3.13",
  "Programming Language :: Python :: 3.14",
]
dependencies = [
  "fhirpathpy>=0.2.2",
  "numpy>=2",
  "pandas>=2",
  "pyjwt>=2.4",
  "requests>=2.31",
  "requests-cache>=0.9.7",
  "tqdm>=4.56",
]
optional-dependencies.all = [
  "dicomweb-client>=0.52",
  "pydicom>=3.0.1",
  "simpleitk>=2.0.2",
  "spacy>=3.0.6",
]
optional-dependencies.downloader = [
  "dicomweb-client>=0.52",
  "pydicom>=2.1.2",
  "simpleitk>=2.0.2",
]
optional-dependencies.miner = [
  "spacy>=3.0.6",
]
urls = { Repository = "https://github.com/UMEssen/FHIR-PYrate" }

[dependency-groups]
dev = [
  "beautifulsoup4>=4.11.1,<5",
  "jupyter>=1,<2",
  "pre-commit>=4.5.1",
  "pytest>=9.0.2",
  "python-dotenv>=1.2.1",
]

[tool.setuptools]
packages.find.include = [ "fhir_pyrate*" ]

[tool.ruff]
target-version = "py310"
# Same as Black
line-length = 88
lint.select = [
  "ARG",  # Unused arguments
  "B",    # flake8-bugbear
  "C",    # flake8-comprehensions
  "D401", # First line of docstring should be in imperative mood
  "E",    # pycodestyle errors
  "EXE",  # flake8-executable
  "F",    # pyflakes
  "G",    # flake8-logging-format
  "I",    # isort
  "N",    # Naming conventions
  "PERF", # perflint
  "PL",   # pylint
  "RUF",  # ruff
  "S",    # flake8-bandit (security)
  "SIM",  # flake8-simplify
  "UP",   # PyUpgrade
  "W",    # pycodestyle warnings
]
lint.ignore = [
  "ARG001", # Unused function argument
  "ARG002", # Unused method argument
  "C901",   # Too complex
  "E501",   # line too long, handled by black
  "N813",   # Camelcase imported as lowercase
  "PLR",    # pylint refactoring
  "S101",   # Use of assert detected
]
lint.unfixable = [
  "F401", # Do not fix unused imports, it's annoying during development
]
lint.pydocstyle.convention = "google"

[tool.mypy]
# Ensure full coverage
check_untyped_defs = true
disallow_untyped_defs = true
disallow_incomplete_defs = true
disallow_untyped_decorators = true
# Restrict dynamic typing
disallow_any_generics = true
disallow_subclassing_any = true
warn_return_any = true
# Know exactly what you're doing
warn_redundant_casts = true
warn_unused_ignores = true
warn_unused_configs = true
warn_unreachable = true
show_error_codes = true

[tool.pytest]
ini_options.testpaths = [ "tests" ]

[tool.markdownlint]
# Disable rules globally
disable = [
  "MD013", # line-length
]

[virtualenvs]
create = true
in-project = true