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

[project]
name = "oneprompt-seg"
version = "1.0.0"
description = "One-Prompt to Segment All Medical Images"
readme = "README.md"
license = {text = "MIT"}
authors = [
    {name = "One-Prompt Team", email = "oneprompt@example.com"}
]
keywords = [
    "medical imaging",
    "image segmentation",
    "deep learning",
    "pytorch",
    "computer vision"
]
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "Intended Audience :: Healthcare Industry",
    "License :: OSI Approved :: MIT License",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.8",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Topic :: Scientific/Engineering :: Artificial Intelligence",
    "Topic :: Scientific/Engineering :: Medical Science Apps.",
]
requires-python = ">=3.8"
dependencies = [
    "torch>=1.10.0",
    "torchvision>=0.11.0",
    "numpy>=1.19.0",
    "pandas>=1.3.0",
    "Pillow>=8.0.0",
    "scikit-image>=0.18.0",
    "scikit-learn>=0.24.0",
    "monai>=0.8.0",
    "einops>=0.4.0",
    "tensorboardX>=2.4.0",
    "tqdm>=4.60.0",
    "python-dateutil>=2.8.0",
    "PyYAML>=5.4.0",
    "matplotlib>=3.3.0",
    "seaborn>=0.11.0",
    "opencv-python>=4.5.0",
]

[project.optional-dependencies]
dev = [
    "pytest>=6.0.0",
    "pytest-cov>=2.12.0",
    "black>=21.0.0",
    "isort>=5.9.0",
    "flake8>=3.9.0",
    "mypy>=0.900",
    "pre-commit>=2.13.0",
]
docs = [
    "sphinx>=4.0.0",
    "sphinx-rtd-theme>=0.5.0",
    "sphinx-autodoc-typehints>=1.12.0",
]

[project.urls]
Homepage = "https://github.com/oneprompt/One-Prompt-Medical-Image-Segmentation"
Documentation = "https://oneprompt-seg.readthedocs.io"
Repository = "https://github.com/oneprompt/One-Prompt-Medical-Image-Segmentation"
Issues = "https://github.com/oneprompt/One-Prompt-Medical-Image-Segmentation/issues"

[project.scripts]
oneprompt-train = "scripts.train:main"
oneprompt-val = "scripts.val:main"

[tool.setuptools.packages.find]
where = ["src"]

[tool.setuptools.package-data]
"*" = ["*.yaml", "*.yml", "*.json"]

# Black configuration
[tool.black]
line-length = 88
target-version = ['py38', 'py39', 'py310', 'py311']
include = '\.pyi?$'
extend-exclude = '''
/(
    \.git
    | \.mypy_cache
    | \.pytest_cache
    | \.venv
    | build
    | dist
    | __pycache__
)/
'''

# isort configuration
[tool.isort]
profile = "black"
line_length = 88
skip_gitignore = true
known_first_party = ["oneprompt_seg"]
known_third_party = ["torch", "torchvision", "numpy", "pandas", "monai"]

# pytest configuration
[tool.pytest.ini_options]
testpaths = ["tests"]
python_files = ["test_*.py"]
python_functions = ["test_*"]
addopts = "-v --tb=short"
filterwarnings = [
    "ignore::DeprecationWarning",
    "ignore::UserWarning",
]

# mypy configuration
[tool.mypy]
python_version = "3.8"
warn_return_any = true
warn_unused_configs = true
ignore_missing_imports = true
exclude = [
    "build",
    "dist",
    "docs",
]

# Coverage configuration
[tool.coverage.run]
source = ["src/oneprompt_seg"]
branch = true
omit = [
    "*/tests/*",
    "*/__pycache__/*",
]

[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",
    "def __repr__",
    "raise AssertionError",
    "raise NotImplementedError",
    "if __name__ == .__main__.:",
]