pyproject.toml

[tool.poetry]
name = "nova-top-level-docs"
version = "0.1.0"
description = "Utilties for accessing the ORNL Galaxy instance"
authors = ["Andrew Ayres <ayresaf@ornl.gov>"]
readme = "README.md"
license = "MIT"
keywords = ["NOVA", "Galaxy", "documentation"]
packages = [
    {include = "nova_top_level_docs", from = "src"}
]


[tool.poetry.dependencies]
python = "^3.10"
bioblend = "^1.3.0"
tomli = "^2.0.2"

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


[tool.pytest.ini_options]
testpaths = ["tests"]
python_files = ["test*.py"]
norecursedirs = [".git", "tmp*", "_tmp*", "__pycache__"]

[tool.ruff]
line-length = 120

[tool.ruff.lint]
select = [
    "E",  # pycodestyle errors
    "W",  # pycodestyle warnings
    "F",  # pyflakes
    "I",  # isort
    "B",  # flake8-bugbear
    "C4",  # flake8-comprehensions
    "N",  # PEP8 naming convetions
    "D"  # pydocstyle
]
ignore = [
    "C901",  # too complex
    "D102", # Missing docstring in public function
    "D103", # Missing docstring in public method
    "D401"  # imperative mood

]

[tool.ruff.lint.extend-per-file-ignores]
'__init__.py' = ['D104'] # Missing docstring in public package



[tool.ruff.lint.pydocstyle]
convention = "numpy"

[tool.mypy]
ignore_missing_imports = false
check_untyped_defs = true
disallow_untyped_defs = true
ignore_errors = false
disable_error_code = ["import-untyped"]
# You can exclude files with the following (ONLY WHEN NECESSARY)
# exclude = ["path/to/file"]

[tool.coverage.report]
omit = [
    '*__init__*', # __init__ files should just re-export other classes and functions
]

[tool.coverage.run]
command_line = "-m pytest --junit-xml=reports/junit.xml"
data_file = "reports/.coverage"

[tool.poetry.dev-dependencies]
mypy = ">=1.10.0"
pre-commit = ">=2.20.0"
coverage = ">=6.4.3"
pytest = "*"
ruff = ">=0.6.2"
copier=">=9.3"
sphinx = "*"
sphinx-rtd-theme = "^3.0.0rc3"
sphinxcontrib-napoleon = "*"
tomli = "^2.0.2"