pyproject.toml

[build-system]
requires = ["setuptools>=61.0", "wheel", "setuptools_scm[toml]>=6.0"]
build-backend = "setuptools.build_meta"

[project]
name = "marEx"
authors = [
    {name = "Aaron Wienkers", email = "aaron@wienkers.com"},
]
description = "Marine Extremes Detection and Tracking"
readme = "README.md"
requires-python = ">=3.10"
classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Intended Audience :: Science/Research",
    "Topic :: Scientific/Engineering :: Atmospheric Science",
    "Topic :: Scientific/Engineering :: Physics",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Operating System :: OS Independent",
    "Operating System :: POSIX :: Linux",
    "Operating System :: MacOS",
    "Operating System :: Microsoft :: Windows",
]
dynamic = ["version"]
dependencies = [
    "numpy",
    "xarray[complete]",
    "dask[complete]==2025.3.0",
    "netcdf4",
    "scipy",
    "scikit-image",
    "dask_image",
    "pandas",
    "numba",
    "pillow",
    "xhistogram",
    "flox>=0.10.1",
    "matplotlib",
    "cartopy",
]

[project.optional-dependencies]
# Minimal installation (basic oceanographic analysis)
minimal = []

# Performance optimisation dependencies
performance = [
    "jax",
    "jaxlib",
]

# High-performance computing cluster support
hpc = [
    "dask_jobqueue",
    "psutil",
]

# Visualisation and plotting
plotting = [
    "seaborn>=0.11.0",
    "cmocean",
    "cartopy",
    "matplotlib>=3.5.0",
    "ffmpeg",
]

# Full installation (all optional dependencies)
full = [
    "jax",
    "jaxlib",
    "dask_jobqueue",
    "seaborn>=0.11.0",
    "cmocean",
    "ffmpeg",
]

# Development tools
dev = [
    "pytest>=7.0.0",
    "pytest-cov",
    "pytest-xdist",
    "black>=22.0.0",
    "flake8>=4.0.0",
    "flake8-pyproject",
    "isort>=5.0.0",
    "mypy>=0.991",
    "pre-commit>=2.20.0",
    "coverage[toml]>=6.0.0",
    "nbqa",
    "bandit[toml]>=1.7.0",
    "psutil",
    "sphinx>=5.0.0",
    "sphinx-rtd-theme",
    "myst-parser",
    "jupyter",
    "ipykernel",
]

# Documentation building
docs = [
    "sphinx>=5.0.0",
    "sphinx-rtd-theme",
    "myst-parser",
    "sphinx-autodoc-typehints",
    "nbsphinx",
    "pandoc",
    "sphinxcontrib-video",
]

# Testing framework
test = [
    "pytest>=7.0.0",
    "pytest-cov",
    "pytest-xdist",
    "coverage[toml]>=6.0.0",
    "psutil",
]

[project.urls]
"Homepage" = "https://github.com/wienkers/marEx"
"Bug Tracker" = "https://github.com/wienkers/marEx/issues"

[tool.setuptools]
packages = ["marEx"]

[tool.setuptools_scm]
version_scheme = "guess-next-dev"
local_scheme = "node-and-date"

[tool.black]
line-length = 132
target-version = ['py310']

[tool.isort]
profile = "black"
line_length = 132

[tool.flake8]
max-line-length = 132
extend-ignore = ["E203", "W503", "E402", "D205", "D400"]
per-file-ignores = [
    "__init__.py:F401",
    "tests/*:D",
]

[tool.pytest.ini_options]
testpaths = ["tests"]
python_files = ["test_*.py"]
python_classes = ["Test*"]
python_functions = ["test_*"]
addopts = [
    "-v",
    "--tb=short",
    "--strict-markers",
    "--disable-warnings",
]
log_cli_level = "WARNING"
log_cli_format = "%(levelname)s %(name)s: %(message)s"
filterwarnings = [
    "ignore::UserWarning",
    "ignore::FutureWarning",
    "ignore::DeprecationWarning",
]
markers = [
    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
    "integration: marks tests as integration tests",
    "benchmark: marks tests as benchmark tests",
    "nocov: marks tests to be excluded from coverage reporting",
    "numba_issue: marks tests that have Numba compatibility issues with coverage",
]

[tool.coverage.run]
source = ["marEx"]
parallel = true  # Enable parallel coverage collection
concurrency = ["thread", "multiprocessing"]  # Handle both threads and processes
sigterm = true  # Handle SIGTERM gracefully
omit = [
    "*/tests/*",
    "*/test_*.py",
    "setup.py",
    "*/_coverage_init.py",
    "*/_dependencies.py",
]

[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",
    "@jit",
    "@njit",
    "@numba\\.jit",  # Add comprehensive Numba exclusions
    "@numba\\.njit",
    "@numba\\.vectorize",
    "@numba\\.guvectorize",
    "def __repr__",
    "if self.debug:",
    "if settings.DEBUG",
    "raise AssertionError",
    "raise NotImplementedError",
    "except ImportError:",
    "if 0:",
    "if __name__ == .__main__.:",
    "class .*\\bProtocol\\):",
    "@(abc\\.)?abstractmethod",
]
show_missing = true
precision = 2

[tool.coverage.html]
directory = "htmlcov"

[tool.mypy]
python_version = "3.10"
warn_return_any = true
warn_unused_configs = true
disallow_untyped_defs = false
disallow_incomplete_defs = false
check_untyped_defs = true
disallow_untyped_decorators = false
no_implicit_optional = true
warn_redundant_casts = true
warn_unused_ignores = true
warn_no_return = true
warn_unreachable = true
strict_equality = true
# Ignore missing imports for scientific packages that often lack stubs
ignore_missing_imports = true
# Exclude test files and notebooks for now
exclude = [
    "tests/",
    "examples/",
    "build/",
    "dist/",
]

[[tool.mypy.overrides]]
module = [
    "numpy.*",
    "scipy.*",
    "pandas.*",
    "xarray.*",
    "dask.*",
    "matplotlib.*",
    "cartopy.*",
    "skimage.*",
    "numba.*",
    "jax.*",
]
ignore_missing_imports = true