[project]
name = "medax-pipeline"
version = "1.0.1"
description = "An ETL pipeline to transfer FHIR data into a graph database"
authors = [
    "Ilya Mazien",
    "Tom Gebhardt",
    "Lea Michaelis",
    "Ron Henkel",
    "Benjamin Winter",
    "Dagmar Waltemath",
    "Judith Wodke"
]

license = "MIT"
readme = "README.md"
requires-python = ">=3.10"
classifiers = [
    "Development Status :: 3 - Alpha",
    "Intended Audience :: Developers",
    "Intended Audience :: Science/Research",
    "Operating System :: OS Independent",
    "Programming Language :: Python",
    "Natural Language :: English",
    "Topic :: Scientific/Engineering :: Medical-Informatics",
]
dependencies = [
    "pyyaml>=5.0",
    "biocypher>=0.16.0,<1.0.0",
    "more-itertools",
    "appdirs",
    "treelib==1.6.4",
    "rdflib>=6.2.0,<7.0.0",
    "networkx>=3.0,<4.0",
    "stringcase>=1.2.0,<2.0.0",
    "neo4j-utils==0.0.7",
    "pandas>=2.0.1,<3.0.0",
    "pooch>=1.7.0,<2.0.0",
    "tqdm>=4.65.0,<5.0.0",
    "requests>=2.31.0,<3.0.0",
    "python-dotenv>=1.0.0,<2.0.0",
    "beautifulsoup4>=4.12.3,<5.0.0",
    "lxml>=5.1.0,<6.0.0",
]

[project.urls]
Homepage = "https://www.medizin.uni-greifswald.de/medizininformatik/research/current-projects/medax/"
Repository = "https://git.uni-greifswald.de/MILA_public/medax_pipeline"

# biocypher is pulled from a feature branch via uv's source override
[tool.uv.sources]
#biocypher = { git = "https://github.com/biocypher/biocypher.git", branch = "feat/dynamic-node-property-headers" } #enable this to test the feature branch again


[tool.uv]
package = false

# Dev dependencies (PEP 735 dependency groups, natively understood by uv)
[dependency-groups]
dev = [
    "sphinx>=5.0.0",
    "sphinx-design>=0.3.0,<0.4.0",
    "sphinx-rtd-theme>=1.0.0",
    "sphinx-last-updated-by-git>=0.3",
    "sphinx-autodoc-typehints>=1.18.0",
    "myst-parser>=0.18.0,<0.19.0",
    "yapf>=0.32.0,<0.33.0",
    "pytest>=6.0",
    "tox>=3.20.1",
    "pre-commit>=2.17.0",
    "bump2version",
    "coverage>=6.0",
    "pytest-cov>=3.0.0,<4.0.0",
    "hypothesis>=6.50.1,<7.0.0",
    "isort>=5.10.1,<6.0.0",
    "ipython>=8.7.0,<9.0.0",
    "ipykernel>=6.23.1,<7.0.0",
    "sphinxext-opengraph>=0.8.2,<0.9.0",
    "coverage-badge>=1.1.0,<2.0.0",
    "nbsphinx>=0.9.2,<0.10.0",
    "black>=23.9.1,<24.0.0",
    "flake8>=6.1.0,<7.0.0",
]

# --- Tool configs below are build-tool-agnostic and carried over unchanged ---

[tool.pytest.ini_options]
testpaths = ["tests"]
addopts = "--ignore=mdm2neo4j"
log_cli = true
log_level = "INFO"
markers = [
    "requires_neo4j: Requires connection to a Neo4j server",
    "requires_postgresql: Requires connection to a PostgreSQL server",
    "inject_driver_args(driver_args): Arguments for the Driver",
]

[tool.black]
line-length = 80
target-version = ['py310']
include = '\.pyi?$'
exclude = '''
(
  /(
      \.eggs
    | \.git
    | \.hg
    | \.mypy_cache
    | \.tox
    | \.venv
    | _build
    | buck-out
    | build
    | dist
  )/
)
'''

[tool.isort]
from_first = true
line_length = 80
multi_line_output = 3
include_trailing_comma = true
use_parentheses = true
known_num = "numpy,pandas"
sections = "FUTURE,STDLIB,THIRDPARTY,NUM,FIRSTPARTY,LOCALFOLDER"
no_lines_before = "LOCALFOLDER"
balanced_wrapping = true
force_grid_wrap = 0
length_sort = "1"
indent = "    "
profile = "black"

[tool.flake8]
ignore = ["E203", "D200", "D202", "D401", "D105", "W504"]
per-file-ignores = [
    "docs/source/conf.py:D100",
    "tests/*:D100,D101,D102",
    "*/__init__.py:F401",
]
max-line-length = 80
count = true