logic-network-generator/pyproject.toml at main · reactome/logic-network-generator · GitHub

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[tool.poetry]
name = "logic-network-generator"
version = "0.1.0"
description = "Generator of pairwise interaction files from Reactome Graph database"
authors = ["Adam Wright <adam.wright@wormbase.org>"]
license = "Apache 2.0"
readme = "README.md"

[tool.poetry.dependencies]
python = "^3.10"
py2neo = "^2021.2.4"
pandas = "^2.2.0"
numpy = "^1.26.3"
pyarrow = "^17.0.0"
scipy = "^1.12.0"
mypy = "^1.8.0"
isort = "^5.13.2"
click = "^8.1.7"
python-dotenv = "^1.2.2"
networkx = "^3.0"

[tool.poetry.group.dev.dependencies]
mypy = "^1.8.0"
pandas-stubs = "^2.1.4.231227"
isort = "^5.10.3"
ruff = "^0.3.4"
pre-commit = "^3.7.0"
pytest = "^9.0.3"
pytest-cov = "^7.0.0"

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

[tool.flake8]
ignore = ""
plugins = ["flake8-mypy"]

[tool.black]
line-length = 88  # Adjust line length as needed
target-version = ['py39']

[tool.pytest.ini_options]
testpaths = ["tests"]
python_files = ["test_*.py"]
python_classes = ["Test*"]
python_functions = ["test_*"]
addopts = [
    "--verbose",
    "--strict-markers",
]
markers = [
    "database: tests that require a live Neo4j connection (excluded from CI)",
    "integration: tests that require artifacts from a prior pathway generation run in output/ (excluded from CI)",
]

[tool.coverage.run]
source = ["src"]
omit = [
    "*/tests/*",
    "*/test_*.py",
]

[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",
    "def __repr__",
    "raise AssertionError",
    "raise NotImplementedError",
    "if __name__ == .__main__.:",
    "if TYPE_CHECKING:",
]