pyproject.toml

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

[project]
name = "muc_one_up"
version = "0.44.4"
description = "MucOneUp: a tool to simulate MUC1 VNTR diploid references"
readme = "README.md"
requires-python = ">=3.10"
license = {text = "MIT"}
authors = [
    {name = "Bernt Popp", email = "bernt.popp.md@gmail.com"},
]
keywords = ["bioinformatics", "genomics", "MUC1", "VNTR", "simulation"]
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 :: Bio-Informatics",
]

dependencies = [
    "click>=8.1.0,<9.0",
    "orfipy>=0.0.3,<1.0",
    "jsonschema>=3.2.0,<5.0",
    "rfc8785>=0.1.2",  # RFC 8785 JSON Canonicalization Scheme for config fingerprinting
    "biopython>=1.80",  # Required for FASTA I/O in read simulation and CLI
]

[project.optional-dependencies]
dev = [
    "pytest>=8.0.0",
    "pytest-cov>=5.0.0",
    "pytest-mock>=3.14.0",  # Required for mocker fixture in tests
    "ruff==0.14.1",  # Pinned version - keep in sync with .pre-commit-config.yaml
    "mypy>=1.8.0",
    "types-jsonschema>=4.0.0",
    "mkdocs-material>=9.5.0",
    "mkdocstrings[python]>=0.24.0",
    "mkdocs-click>=0.8.0",
    "pymdown-extensions>=10.7",
]

docs = [
    "mkdocs-material>=9.5.0",
    "mkdocstrings[python]>=0.24.0",
    "mkdocs-click>=0.8.0",
    "pymdown-extensions>=10.7",
]

[project.scripts]
muconeup = "muc_one_up.cli.click_main:main"

[project.urls]
Homepage = "https://github.com/berntpopp/MucOneUp"
Repository = "https://github.com/berntpopp/MucOneUp"
Issues = "https://github.com/berntpopp/MucOneUp/issues"
Documentation = "https://berntpopp.github.io/MucOneUp/"

# ==================== RUFF ====================
[tool.ruff]
target-version = "py310"
line-length = 100
indent-width = 4

# Exclude build artifacts and caches
exclude = [
    ".git",
    ".mypy_cache",
    ".pytest_cache",
    ".ruff_cache",
    "__pycache__",
    "build",
    "dist",
    "*.egg-info",
]

[tool.ruff.lint]
# Select comprehensive rule set
select = [
    "E",      # pycodestyle errors
    "W",      # pycodestyle warnings
    "F",      # Pyflakes
    "UP",     # pyupgrade
    "B",      # flake8-bugbear
    "SIM",    # flake8-simplify
    "I",      # isort
    "N",      # pep8-naming
    "C4",     # flake8-comprehensions
    "PTH",    # flake8-use-pathlib
    "RUF",    # Ruff-specific rules
]

ignore = [
    "E501",   # Line too long (handled by formatter)
    "B008",   # Do not perform function calls in argument defaults
    "N802",   # Function name should be lowercase (bioinformatics conventions)
    "SIM115", # Use context manager for opening files (legacy code style)
    "SIM113", # Use enumerate for index variables (not always clearer)
    "PTH123", # Use Path.open() instead of open() (backwards compatibility)
]

# Allow autofix for all enabled rules
fixable = ["ALL"]
unfixable = []

# Allow unused variables when underscore-prefixed
dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"

[tool.ruff.lint.per-file-ignores]
"tests/*" = ["S101", "ARG", "PLR2004"]  # Allow asserts, unused args, magic values
"__init__.py" = ["F401"]  # Allow unused imports in __init__
"helpers/*" = ["N817"]  # Allow common acronyms like ET for ElementTree
"scripts/*" = ["RUF001"]  # Allow multiplication sign × in documentation strings

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

[tool.ruff.format]
quote-style = "double"
indent-style = "space"
skip-magic-trailing-comma = false
line-ending = "auto"

# ==================== MYPY ====================
[tool.mypy]
python_version = "3.10"
warn_return_any = true
warn_unused_configs = true
warn_redundant_casts = true
warn_unused_ignores = true
warn_no_return = true
strict_equality = true
check_untyped_defs = true

# Start with gradual typing - can be made stricter over time
disallow_untyped_defs = false
disallow_incomplete_defs = false
no_implicit_optional = true

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

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

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

[[tool.mypy.overrides]]
module = "tests.*"
disallow_untyped_defs = false

[[tool.mypy.overrides]]
module = "muc_one_up.bioinformatics.validation"
warn_unreachable = false  # False positive with regex pattern matching

[[tool.mypy.overrides]]
module = "rfc8785"
ignore_missing_imports = true

# ==================== PYTEST ====================
[tool.pytest.ini_options]
testpaths = ["tests"]
python_files = ["test_*.py"]
python_classes = ["Test*"]
python_functions = ["test_*"]
addopts = [
    "-v",
    "--strict-markers",
    "--cov=muc_one_up",
    "--cov-report=term-missing",
    "--cov-report=html",
    "--cov-report=xml",
]
markers = [
    "unit: marks tests as unit tests (fast, isolated)",
    "integration: marks tests as integration tests (slower, multiple components)",
    "slow: marks tests as slow-running (> 1 second)",
    "cli: marks tests as CLI interface tests",
    "bioinformatics: marks tests as bioinformatics-specific (sequence validation, etc.)",
    "requires_tools: marks tests that require specific external tools to be available",
    "e2e: marks end-to-end tests requiring real bioinformatics tools (not run in CI)",
]

# ==================== COVERAGE ====================
[tool.coverage.run]
source = ["muc_one_up"]
branch = true
omit = [
    "*/tests/*",
    "*/__pycache__/*",
    "*/site-packages/*",
]

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