pyproject.toml

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

[project]
name = "ensembl_genes"
version = "0.0.0"
description = "Extract the Ensembl gene catalog to simple tables."
authors = [
    {name = "Related Sciences Data Team"}
]
readme = "README.md"
license = {text = "Apache-2.0"}
requires-python = ">=3.10"
dependencies = [
    "pyarrow>=7.0.0",
    "typer[all]>=0.9.0",
    "jupyter>=1.0.0",
    "mysql-connector-python>=8.0.26",
    "nbconvert>=6.2.0",
    "notebook>=6.4.4",
    "openpyxl>=3.0.9",
    "pandas>=1.3.3",
    "papermill>=2.3.3",
    "requests>=2.26.0",
    "sqlalchemy>=1.4.25",
    "tabulate>=0.8.9",
    "bioregistry>=0.9.64",
]

[project.optional-dependencies]
dev = [
    "pre-commit>=4.1.0",
    "pytest>=6.2.5",
]

[project.urls]
repository = "https://github.com/related-sciences/ensembl-genes"

[project.scripts]
ensembl_genes = "ensembl_genes.commands:Commands.command"

[tool.setuptools.package-data]
ensembl_genes = [
    "queries/*.sql",
    "notebooks/*.ipynb"
]

[tool.ruff]
target-version = "py310"
ignore = [
    "E501",  # line-too-long (black should handle)
]
line-length = 88
select = [
    "B",  # flake8-bugbear
    "C",  # flake8-comprehensions
    "C90",  # mccabe
    "E",  # pycodestyle errors
    "F",  # pyflakes
    "I",  # isort
    "UP",  # pyupgrade
    "W",  # pycode warnings
]

[tool.mypy]
python_version = "3.10"
strict = true
pretty = true
show_error_context = true

# https://mypy.readthedocs.io/en/stable/config_file.html#using-a-pyproject-toml-file
[[tool.mypy.overrides]]
module = [
    "bioregistry.*",
    "pandas.*",
    "papermill.*",
    "requests.*",
    "sqlalchemy.*",
]
ignore_missing_imports = true