poppy/pyproject.toml at main · RomanoLab/poppy · GitHub

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[build-system]
requires = ["setuptools>=68", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "poppy"
version = "0.1.0"
description = "Phyto-Ontology Platform for Pharmacology"
readme = "README.md"
requires-python = ">=3.10"
authors = [{ name = "Oresta S. I. Hewryk et al." }]
license = { text = "MIT" }
dependencies = [
  "requests>=2.32",
  "pandas>=2.2",
  "polars>=1.5",
  "numpy>=1.26",
  "rdflib>=7.0",
  "pyyaml>=6.0",
  "scikit-learn>=1.5",
  "matplotlib>=3.9",
  "tqdm>=4.66",
  "biopython>=1.84",
  "psycopg2-binary>=2.9"
]

[project.optional-dependencies]
chem = [
  "rdkit-pypi>=2022.9.5"
]

dev = [
  "pytest>=8.0",
  "pytest-cov>=5.0",
  "ruff>=0.6",
  "black>=24.0",
  "mypy>=1.10",
  "pre-commit>=3.7",
]


[tool.black]
line-length = 100

[tool.pytest.ini_options]
testpaths = ["tests"]
addopts = "-q"


[tool.ruff]

extend-exclude = ["notebooks/**", "src/poppy/literature/pubmed_impl.py"]

[tool.ruff.per-file-ignores]

"notebooks/**" = ["E402","F821","F401","E702","E701","F811","F841","E722","F541"]
"src/poppy/literature/pubmed_impl.py" = ["E402","F821","E401","E702","E701"]