DNANet/pyproject.toml at main · NetherlandsForensicInstitute/DNANet · GitHub

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[project]
name = "DNANet"
version = "0.1.0"
description = " An open source repository offering tools for parsing DNA profiles and integrating machine learning models."

dependencies = [
    "numpy>=2.2.4",
    "scipy>=1.15.1",
    "tqdm>=4.67.1",
    "confidence>=0.15",
    "torch>=2.5.1",
    "torchmetrics>=1.7.1",
    "construct>=2.10.70",
    "datasets>=4.0.0",
    "matplotlib>=3.10.1",
    "mlflow>=2.21.3",
    "tensorboard>=2.18.0",
    "huggingface-hub[hf_xet]>=0.35.0",
    "coolname>=2.2.0",
    "openpyxl>=3.1.5",
    "pydantic>=2.12.5",
    "pydantic-numpy>=8.0.1",
    "loguru>=0.7.3",
]
requires-python = ">=3.10,<=3.12"
readme = "README.md"
license = {text = "Apache-2.0"}


[dependency-groups]
testing = [
    "pytest>=8.3.5",
    "pytest-cov>=7.0.0",
    "pytest-xdist>=3.8.0",
]
quality = [
    "ruff>=0.15.5",
    "mypy>=1.19.1",
]

[tool.pytest.ini_options]
pythonpath = "."
addopts = "--cov --cov-report=term"
source = ["."]

[tool.coverage.run]
branch = true
omit = [
    "tests/*",
    "*__init__.py"
]

[tool.coverage.report]
skip_empty = true
show_missing = true

exclude_also = [
    "def __repr__",
    "if self\\.debug",

    "raise AssertionError",
    "raise NotImplementedError",

    "if 0:",
    "if __name__ == .__main__.:",

    "@(abc\\.)?abstractmethod",
]
ignore_errors = true


##### LINT & FORMAT #####
[tool.ruff]
extend-exclude = [
    ".venv"
]
line-length = 101

[tool.ruff.format]
quote-style = "single"
skip-magic-trailing-comma = false

[tool.ruff.lint]
# Rules: 'https://docs.astral.sh/ruff/rules'
select = [
    "I",  # Imports
    "B",  # Bugbear,
    "D",  # Docstyles
    "NPY",  # Numpy
    "TC",  # Type Checking
]
exclude = ["tests/*"]
ignore = ["D100"]
fixable = ["ALL"]
unfixable = []

[tool.ruff.lint.per-file-ignores]
"__init__.py" = ["E402", "D104"]
"**/{tests,docs}/*" = ["E402", "D"]

[tool.ruff.lint.isort]
length-sort = true
lines-after-imports = 2

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

[tool.mypy]
disable_error_code = ["import-untyped"]
[tool.pdm]
distribution = false

[tool.pdm.scripts]
test = "pdm run pytest"
lint = "pdm run ruff check ."
format = "pdm run ruff format --check ."
typing = "pdm run mypy"