pyproject.toml

[build-system]
requires = ["setuptools>=61.0", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "mlscorecheck"
version = "1.0.3"
description = "ML score check: checking the validity of machine learning and computer vision scores"
readme = "README.rst"
requires-python = ">=3.10"
license = {text = "MIT"}
authors = [
    {name = "Gyorgy Kovacs", email = "gyuriofkovacs@gmail.com"},
]
maintainers = [
    {name = "Gyorgy Kovacs", email = "gyuriofkovacs@gmail.com"},
]
keywords = ["machine learning", "computer vision", "score validation", "consistency checking"]
classifiers = [
    "Development Status :: 3 - Alpha",
    "Intended Audience :: Science/Research",
    "Intended Audience :: Developers",
    "License :: OSI Approved :: MIT License",
    "Programming Language :: Python",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Topic :: Scientific/Engineering :: Artificial Intelligence",
    "Topic :: Software Development",
    "Operating System :: Microsoft :: Windows",
    "Operating System :: POSIX",
    "Operating System :: Unix",
    "Operating System :: MacOS",
]
dependencies = [
    "numpy",
    "scipy",
    "scikit-learn",
    "pulp",
]

[project.optional-dependencies]
tests = ["pytest"]
docs = [
    "sphinx",
    "sphinx-gallery",
    "sphinx_rtd_theme",
    "matplotlib",
    "pandas",
    "pulp",
]
dev = [
    "pytest",
    "sphinx",
    "sphinx-gallery",
    "sphinx_rtd_theme",
    "matplotlib",
    "pandas",
    "pulp",
]

[project.urls]
Homepage = "https://github.com/gykovacs/mlscorecheck"
Repository = "https://github.com/gykovacs/mlscorecheck"
Documentation = "https://mlscorecheck.readthedocs.io/"
"Bug Tracker" = "https://github.com/gykovacs/mlscorecheck/issues"

[tool.setuptools]
packages = ["mlscorecheck"]
include-package-data = true

[tool.setuptools.package-data]
mlscorecheck = [
    "individual/solutions.json",
    "scores/scores.json",
    "experiments/machine_learning/common_datasets.json",
    "experiments/machine_learning/sklearn.json",
    "experiments/ehg/tpehg.json",
    "experiments/retina/drive/drive_1_test_fov.json",
    "experiments/retina/drive/drive_1_test_all.json",
    "experiments/retina/drive/drive_1_train_fov.json",
    "experiments/retina/drive/drive_1_train_all.json",
    "experiments/retina/drive/drive_2_test_fov.json",
    "experiments/retina/drive/drive_2_test_all.json",
    "experiments/retina/drive/drive_2_train_fov.json",
    "experiments/retina/drive/drive_2_train_all.json",
    "experiments/retina/chase_db1/manual1.json",
    "experiments/retina/chase_db1/manual2.json",
    "experiments/retina/diaretdb0/diaretdb0.json",
    "experiments/retina/diaretdb1/diaretdb1.json",
    "experiments/retina/drishti_gs/drishti_gs_test.json",
    "experiments/retina/drishti_gs/drishti_gs_train.json",
    "experiments/retina/hrf/with_fov.json",
    "experiments/retina/hrf/without_fov.json",
    "experiments/retina/stare/ah.json",
    "experiments/retina/stare/vk.json",
    "experiments/skinlesion/isic2016/isic2016.json",
    "experiments/skinlesion/isic2017/isic2017.json",
    "experiments/skinlesion/isic2017/isic2017m.json",
    "experiments/skinlesion/isic2017/isic2017sk.json",
]

# Linting and Code Quality Tools Configuration

[tool.ruff.lint]
select = [
    "E",   # pycodestyle errors
    "W",   # pycodestyle warnings  
    "F",   # pyflakes
    "I",   # isort
    "N",   # pep8-naming
    "UP",  # pyupgrade
    "B",   # flake8-bugbear
    "C4",  # flake8-comprehensions
    "PIE", # flake8-pie
    "SIM", # flake8-simplify
]
ignore = [
    # Allow star imports for package __init__.py files
    "F403",  # `from .module import *` used; unable to detect undefined names
    "F405",  # name may be undefined, or defined from star imports
    # Scientific computing conventions
    "N803",  # argument name should be lowercase (e.g., N, tp, tn)
    "N806",  # variable in function should be lowercase
    # Allow complexity for scientific algorithms
    "C901",  # too complex
    # Allow magic values in scientific contexts
    "PLR2004",  # Magic value used in comparison
]

[tool.ruff]
line-length = 100
target-version = "py310"

[tool.ruff.lint.per-file-ignores]
# Allow star imports and unused imports in __init__.py files
"**/__init__.py" = ["F401", "F403", "F405"]
# Allow star imports in test files  
"tests/**" = ["F401", "F403", "F405", "S101"]
# Allow long lines in mathematical formula files
"**/individual/_tptn_solutions.py" = ["E501"]
# Allow long lines in docstrings for score lists
"**/check/bundles/**/*.py" = ["E501"]
"**/check/multiclass/**/*.py" = ["E501"]

[tool.ruff.lint.isort]
known-first-party = ["mlscorecheck"]

[tool.mypy]
python_version = "3.10"
strict = true
ignore_missing_imports = true
warn_unused_configs = true
exclude = [
    "build",
    "dist", 
    "docs",
    ".eggs",
    "legacy",
]

# Strategic overrides for specific error types that would require extensive refactoring
[[tool.mypy.overrides]]
module = [
    "mlscorecheck.*",
]
disable_error_code = [
    # "no-untyped-def",      # Function definitions without type annotations
    "no-untyped-call",     # Calls to untyped functions  
    "type-arg",            # Missing type parameters for generics like dict, list
]

[tool.pylint.messages_control]
disable = [
    "too-many-arguments",
    "too-many-locals",
    "too-many-branches", 
    "too-many-statements",
    "too-many-return-statements",
    "too-few-public-methods",
    "import-error",
    "no-member",
    "invalid-name",
    "missing-docstring",
    "unused-import",
    "wildcard-import",
    "unused-wildcard-import",
]

[tool.pylint.basic]
good-names = ["i", "j", "k", "n", "p", "tp", "tn", "fp", "fn", "N", "p4"]

[tool.pylint.similarities]
min-similarity-lines = 30

[tool.pytest.ini_options]
testpaths = ["tests"]
pythonpath = ["."]