[tool.poetry]
name = "MeDaX pipeline"
version = "1.0.0"
description = "A unifying framework for biomedical research knowledge graphs"
authors = [
    "Ilya Mazien",
    "Tom Gebhardt",
    "Lea Michaelis",
    "Ron Henkel",
    "Benjamin Winter",
    "Dagmar Waltemath",
    "Judith Wodke"
]
license = "MIT"
packages = [
    { include = "biocypher" }
]
classifiers = [
    "Development Status :: 3 - Alpha",
    "Intended Audience :: Developers",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Operating System :: OS Independent",
    "Programming Language :: Python",
    "Natural Language :: English",
    "Topic :: Scientific/Engineering :: Bio-Informatics"
]
repository = "https://github.com/biocypher/biocypher"
readme = "README.md"

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

[tool.poetry.dependencies]
python = "^3.9"
PyYAML = ">=5.0"
more_itertools = "*"
appdirs = "*"
treelib = "1.6.4"
rdflib = "^6.2.0"
networkx = "^3.0"
stringcase = "^1.2.0"
neo4j-utils = "0.0.7"
pandas = "^2.0.1"
pooch = "^1.7.0"
tqdm = "^4.65.0"

[tool.poetry.group.dev.dependencies]
sphinx = ">=5.0.0"
sphinx-design = "^0.3.0"
sphinx-rtd-theme = ">=1.0.0"
sphinx-last-updated-by-git = ">=0.3"
sphinx-autodoc-typehints = ">=1.18.0"
myst-parser = "^0.18.0"
yapf = "^0.32.0"
pytest = ">=6.0"
tox = ">=3.20.1"
pre-commit = ">=2.17.0"
bump2version = "*"
coverage = ">=6.0"
pytest-cov = "^3.0.0"
hypothesis = "^6.50.1"
isort = "^5.10.1"
ipython = "^8.7.0"
ipykernel = "^6.23.1"
sphinxext-opengraph = "^0.8.2"
coverage-badge = "^1.1.0"
nbsphinx = "^0.9.2"
black = "^23.9.1"
flake8 = "^6.1.0"

[build-system]
requires = ["poetry-core<2.0.0"]
build-backend = "poetry.core.masonry.api"

[tool.poetry.urls]
"Bug Tracker" = "https://github.com/biocypher/biocypher/issues"

[tool.pytest.ini_options]
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