pyproject.toml

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

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

[project]
name = "seu-injection-framework"
version = "1.1.12"
description = "Framework for Single Event Upset (SEU) injection in neural networks for harsh environment applications"
authors = [
    {name = "William Dennis", email = "wwdennis.home@gmail.com"}
]
readme = "README.md"
license = {text = "MIT"}
homepage = "https://github.com/wd7512/seu-injection-framework"
repository = "https://github.com/wd7512/seu-injection-framework"
keywords = ["machine-learning", "robustness", "fault-tolerance", "seu", "radiation", "neural-networks"]
classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Intended Audience :: Science/Research",
    "Intended Audience :: Developers",
    "License :: OSI Approved :: MIT License",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3 :: Only",
    "Topic :: Scientific/Engineering :: Artificial Intelligence",
    "Topic :: Scientific/Engineering :: Physics",
    "Topic :: Software Development :: Libraries :: Python Modules",
    "Topic :: Software Development :: Testing",
    "Environment :: GPU :: NVIDIA CUDA",
    "Natural Language :: English",
    "Typing :: Typed",
]
requires-python = ">=3.9"

# Core dependencies (intentionally slimmed; heavier analysis libs moved to extras)
dependencies = [
    "torch>=2.0.0",
    "numpy>=1.21.0,<2.0.0",
    "tqdm>=4.60.0",
]

[project.optional-dependencies]
# Development & testing (includes analysis libs to keep tests stable)
dev = [
    "pytest>=7.0.0",
    "pytest-cov>=4.0.0",
    "ruff>=0.1.0",
    "bandit>=1.7.0",
    "psutil>=7.1.3",
    "scikit-learn>=1.1.0",
    "pandas>=1.4.0",
    "matplotlib>=3.5.0",
    "seaborn>=0.11.0",
    "scikit-image>=0.19.0",
    "statsmodels>=0.13.0",
    "joblib>=1.1.0",
    "torchvision>=0.15.0",
    "mdformat>=0.7.22",
    "mdformat-gfm>=0.4.1",
    "mdformat-toc>=0.5.0",
    "scipy>=1.8.0",
    "ty>=0.0.1a28",
]

# Analysis & extended research stack
analysis = [
    "scikit-learn>=1.1.0",
    "pandas>=1.4.0",
    "matplotlib>=3.5.0",
    "seaborn>=0.11.0",
    "scikit-image>=0.19.0",
    "statsmodels>=0.13.0",
    "joblib>=1.1.0",
]

# Vision / model zoo extras
vision = [
    "torchvision>=0.15.0",
]

# Notebook / interactive usage
notebooks = [
    "jupyter>=1.0.0",
    "jupyterlab>=3.0.0",
    "ipywidgets>=7.0.0",
]

# Documentation toolchain (optional)
docs = [
    "sphinx>=7.0.0",
    "sphinx-rtd-theme>=2.0.0",
    "sphinx-autodoc-typehints>=1.25.0",
    "myst-parser>=2.0.0",
]

# Examples
examples = [
    "kagglehub>=0.1.0"
]

# Aggregate convenience extra
all = [
    "seu-injection-framework[dev,analysis,vision,notebooks,docs,examples]"
]

[project.urls]
"Homepage" = "https://github.com/wd7512/seu-injection-framework"
"Documentation" = "https://wd7512.github.io/seu-injection-framework/"
"Repository" = "https://github.com/wd7512/seu-injection-framework"
"Bug Tracker" = "https://github.com/wd7512/seu-injection-framework/issues"
"Changelog" = "https://github.com/wd7512/seu-injection-framework/blob/main/CHANGELOG.md"
"Research Paper" = "https://research-information.bris.ac.uk/en/publications/a-framework-for-developing-robust-machine-learning-models-in-hars"
"Download" = "https://pypi.org/project/seu-injection-framework/"



# Tool configurations for code quality
# TODO PIPELINE FIX: Coverage configuration addressed per PIPELINE_FIX_URGENT.md
# ISSUE: Global --cov-fail-under=50 in pytest addopts breaks isolated test runs (benchmarks get 23% coverage)
# SOLUTION IMPLEMENTED: Removed global threshold, now enforced only in CI/CD for full test suite
# CURRENT STATUS: Full test suite achieves 94% coverage (well above 50% minimum requirement)
# ENFORCEMENT: CI/CD pipeline enforces --cov-fail-under=50 on complete test runs only
# BENEFIT: Allows individual test files and benchmark tests to run without coverage failures
# REFERENCE: See .github/workflows/python-tests.yml for CI/CD enforcement implementation

[tool.pytest.ini_options]
testpaths = ["tests"]
python_files = ["test_*.py"]
python_classes = ["Test*"]
python_functions = ["test_*"]
addopts = [
    "--cov=src/seu_injection", 
    "--cov-report=term-missing",
    "--cov-report=html:htmlcov",
    # TODO: --cov-fail-under=50 REMOVED from global config per pipeline fix
    # REASON: Benchmark tests achieve 23% coverage when run isolated, failing 50% threshold
    # CURRENT: Coverage threshold enforced in CI/CD for full suite only (94% > 50%)
    # Note: Coverage threshold removed from default addopts to allow individual test file runs
    # Use --cov-fail-under=50 when running full test suite if desired
    "-v",
    "--tb=short",
    "--strict-markers"
]
markers = [
    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
    "integration: marks tests as integration tests",
    "smoke: marks tests as smoke tests for quick validation",
    "gpu: marks tests that require GPU/CUDA",
]
filterwarnings = [
    "ignore::DeprecationWarning",
    "ignore::PendingDeprecationWarning",
]

[tool.coverage.run]
source = ["src/seu_injection"]
omit = [
    "*/tests/*",
    "*/test_*.py",
    "*/__pycache__/*",
    "*/conftest.py",
    "*/utils/device.py",
    "*/utils/__init__.py",
]

[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",
    "def __repr__",
    "if self.debug:",
    "if settings.DEBUG",
    "raise AssertionError",
    "raise NotImplementedError",
    "if 0:",
    "if __name__ == .__main__.:",
    "class .*\\bProtocol\\):",
    "@(abc\\.)?abstractmethod",
]

# Ruff configuration for linting and formatting
[tool.ruff]
line-length = 88
target-version = "py39"
src = ["src", "tests"]
extend-exclude = ["*.ipynb"]

[tool.ruff.lint]
select = [
    "E",   # pycodestyle errors
    "W",   # pycodestyle warnings  
    "F",   # pyflakes
    "I",   # isort
    "N",   # pep8-naming
    "UP",  # pyupgrade
    "B",   # flake8-bugbear
    "A",   # flake8-builtins
    "C4",  # flake8-comprehensions
    "T20", # flake8-print
]
ignore = [
    "E501",  # Line too long (handled by formatter)
    "B008",  # Do not perform function calls in argument defaults
    "B905",  # zip strict argument
    "N806",  # Variable name in function should be lowercase (allow ML conventions like X, y)
    "T201",  # Print found (allow for debugging/standalone scripts)
    "B011",  # Do not use assert False (pytest uses this pattern)
    "F401",  # Imported but unused (some imports are for testing availability)
]

[tool.ruff.format]
quote-style = "double"
indent-style = "space"

[tool.ty.src]
exclude = ["**/*_legacy*.py"]