pyproject.toml

[project]
name = "stroke-deepisles-demo"
version = "0.1.0"
description = "Demo: HF datasets + DeepISLES stroke segmentation + Gradio visualization"
readme = "README.md"
license = { text = "MIT" }
requires-python = ">=3.11"
authors = [
    { name = "stroke-deepisles-demo contributors" }
]
classifiers = [
    "Development Status :: 3 - Alpha",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Topic :: Scientific/Engineering :: Medical Science Apps.",
]
keywords = ["stroke", "neuroimaging", "segmentation", "BIDS", "NIfTI", "deep-learning"]

dependencies = [
    # Core - pinned to Tobias's fork for BIDS + NIfTI lazy loading (commit c1c15aa)
    "datasets @ git+https://github.com/CloseChoice/datasets.git@c1c15aaa4f00f28f1916f3a896283494162eac49",
    "huggingface-hub>=0.25.0",

    # NIfTI handling
    "nibabel>=5.2.0",
    "numpy>=1.26.0,<2.0.0",

    # Configuration
    "pydantic>=2.5.0",
    "pydantic-settings>=2.1.0",

    # UI (Gradio 6.x - Dec 2025 stable)
    "gradio>=6.0.0,<7.0.0",
    "matplotlib>=3.8.0",

    # Networking
    "requests>=2.0.0",
]

[project.scripts]
stroke-demo = "stroke_deepisles_demo.cli:main"

[dependency-groups]
dev = [
    "pytest>=8.0.0",
    "pytest-cov>=4.1.0",
    "pytest-mock>=3.12.0",
    "pytest-timeout>=2.3.0",
    "mypy>=1.19.0",
    "ruff>=0.14.0",
    "pre-commit>=3.6.0",
    # Type stubs
    "types-requests",
]

[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[tool.hatch.metadata]
allow-direct-references = true

[tool.hatch.build.targets.wheel]
packages = ["src/stroke_deepisles_demo"]

# ─────────────────────────────────────────────────────────────────
# Tool configurations
# ─────────────────────────────────────────────────────────────────

[tool.ruff]
target-version = "py312"
line-length = 100
src = ["src", "tests"]

[tool.ruff.lint]
select = [
    "E",      # pycodestyle errors
    "W",      # pycodestyle warnings
    "F",      # pyflakes
    "I",      # isort
    "B",      # flake8-bugbear
    "C4",     # flake8-comprehensions
    "UP",     # pyupgrade
    "ARG",    # flake8-unused-arguments
    "SIM",    # flake8-simplify
    "TCH",    # flake8-type-checking
    "PTH",    # flake8-use-pathlib
    "RUF",    # ruff-specific
]
ignore = [
    "E501",   # line too long (handled by formatter)
]

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

[tool.mypy]
python_version = "3.12"
strict = true
warn_return_any = true
warn_unused_ignores = true
disallow_untyped_defs = true
plugins = ["pydantic.mypy"]

[[tool.mypy.overrides]]
module = [
    "nibabel.*",
    "gradio.*",
    "datasets.*",
    "niivue.*",
    "numpy.*",
    "pytest.*",
    # DeepISLES modules (only available in DeepISLES Docker image)
    "src.isles22_ensemble",
]
ignore_missing_imports = true

[tool.pytest.ini_options]
testpaths = ["tests"]
python_files = ["test_*.py"]
python_functions = ["test_*"]
addopts = [
    "-v",
    "--tb=short",
    "--strict-markers",
    "-m", "not integration",  # Skip integration tests by default
]
markers = [
    "integration: marks tests requiring external resources (Docker, network)",
    "slow: marks tests that take >10s to run",
]
filterwarnings = [
    "ignore::DeprecationWarning",
]

[tool.coverage.run]
source = ["src/stroke_deepisles_demo"]
branch = true

[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",
    "if TYPE_CHECKING:",
    "raise NotImplementedError",
]