pyproject.toml

[build-system]
requires = ["setuptools>=65.0", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "paraprof"
version = "1.0.0"
description = "Parallel profile likelihood computation using grid-based optimization"
readme = "README.md"
requires-python = ">=3.10"
license = {text = "MIT"}
authors = [
    {name = "Anders Kvellestad", email = "anders.kvellestad@fys.uio.no"},
]
maintainers = [
    {name = "Anders Kvellestad", email = "anders.kvellestad@fys.uio.no"},
]
keywords = [
    "parallel computing",
    "profile likelihood",
    "differential evolution",
    "mpi",
    "optimization",
    "statistical inference",
]
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Topic :: Scientific/Engineering",
    "Topic :: Scientific/Engineering :: Mathematics",
    "Topic :: Scientific/Engineering :: Physics",
    "Operating System :: OS Independent",
]

# Core dependencies
dependencies = [
    "numpy>=1.21",
    "scipy>=1.7",
    "mpi4py>=3.1",
]

[project.optional-dependencies]
# Visualization dependencies (optional)
viz = [
    "matplotlib>=3.5",
]

# Clustering for multi-modal grid refinement (optional)
clustering = [
    "scikit-learn>=1.3.0",
]

# HDF5 binary sample files (optional)
hdf5 = [
    "h5py>=3.0",
]

# Development dependencies
dev = [
    "pytest>=7.0",
    "pytest-cov>=4.0",
    "black>=23.0",
    "ruff>=0.1.0",
    "mypy>=1.0",
    "pre-commit>=3.0",
]

# Documentation dependencies
docs = [
    "sphinx>=6.0",
    "sphinx-rtd-theme>=1.2",
    "sphinx-autodoc-typehints>=1.22",
]

# All optional dependencies
all = [
    "paraprof[viz,clustering,hdf5,dev,docs]",
]

[project.urls]
Homepage = "https://github.com/anderkve/paraprof"
Documentation = "https://paraprof.readthedocs.io"
Repository = "https://github.com/anderkve/paraprof"
Issues = "https://github.com/anderkve/paraprof/issues"
Changelog = "https://github.com/anderkve/paraprof/blob/main/CHANGELOG.md"

[tool.setuptools]
# Use src layout
packages = ["paraprof", "paraprof.jobs"]
package-dir = {"" = "src"}

[tool.setuptools.package-data]
paraprof = ["py.typed"]

# Black configuration
[tool.black]
line-length = 100
target-version = ['py310', 'py311', 'py312']
include = '\.pyi?$'
extend-exclude = '''
/(
  # directories
  \.eggs
  | \.git
  | \.mypy_cache
  | \.pytest_cache
  | \.venv
  | build
  | dist
  | examples
)/
'''

# Ruff configuration
[tool.ruff]
line-length = 100
target-version = "py310"
select = [
    "E",    # pycodestyle errors
    "W",    # pycodestyle warnings
    "F",    # pyflakes
    "I",    # isort
    "N",    # pep8-naming
    "UP",   # pyupgrade
    "B",    # flake8-bugbear
    "C4",   # flake8-comprehensions
    "SIM",  # flake8-simplify
]
ignore = [
    "E501",  # line too long (handled by black)
    "B008",  # do not perform function calls in argument defaults
    "C901",  # too complex
]
exclude = [
    ".git",
    "__pycache__",
    ".pytest_cache",
    ".mypy_cache",
    "build",
    "dist",
    "examples",
    "tests",
]

[tool.ruff.per-file-ignores]
"__init__.py" = ["F401"]  # Allow unused imports in __init__.py

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

# MyPy configuration
[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
no_implicit_optional = true
warn_redundant_casts = true
warn_unused_ignores = true
warn_no_return = true
strict_equality = true
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = "paraprof.*"
ignore_missing_imports = true

# Pytest configuration
[tool.pytest.ini_options]
minversion = "7.0"
addopts = [
    "-ra",
    "--strict-markers",
    "--strict-config",
    "--showlocals",
]
testpaths = ["tests"]
python_files = ["test_*.py"]
python_classes = ["Test*"]
python_functions = ["test_*"]

# Coverage configuration
[tool.coverage.run]
source = ["src"]
omit = [
    "tests/*",
    "*/test_*.py",
]

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