pyproject.toml

[project]
name = "BioStructBenchmark"
version = "0.0.1"
description = "A tool for analyzing protein-nucleic acid complexes"
authors = [
    { name="Delta Kapp", email="deltakapp@gmail.com"},
    { name="Morgan Esler", email="mesler1397@gmail.com"}
]
readme = {file = "README.md", content-type = "text/markdown"}
license = "MIT"
requires-python = ">=3.13.0"
classifiers = [
    "Programming Language :: Python :: 3",
    "Operating System :: OS Independent",
]
dependencies = [
    "biopython>=1.85",
    "numpy>=2.3.1",
    "pandas>=2.0.0"
]

[project.urls]
"Homepage" = "https://github.com/BioStructBenchmark/BioStructBenchmark"

[project.scripts]
biostructbenchmark = "biostructbenchmark.__main__:main"

[build-system]
requires = ["setuptools>=80.9.0"]
build-backend = "setuptools.build_meta"

[tool.setuptools.packages.find]
where = ["."]
include = ["biostructbenchmark*"]
exclude = ["tests*", "output_test*", "*output*"]

[dependency-groups]
test = [
    "pytest>=8.3.0",
    "pytest-cov>=6.0.0",
]
lint = [
    "ruff>=0.8.0",
    "mypy>=1.13.0",
]
security = [
    "bandit>=1.8.0",
    "pip-audit>=2.7.0",
]
quality = [
    "interrogate>=1.7.0",
    "vulture>=2.14",
]
dev = [
    {include-group = "test"},
    {include-group = "lint"},
    {include-group = "security"},
    {include-group = "quality"},
    "pre-commit>=4.0.0",
    "twine>=6.1.0",
]

[tool.pytest.ini_options]
minversion = "8.0"
addopts = [
    "-ra",
    "-q",
    "--strict-markers",
    "--cov=biostructbenchmark",
    "--cov-report=term-missing",
    "--cov-report=html",
    "--cov-fail-under=80",
]
pythonpath = "."
testpaths = ["tests"]
markers = [
    "integration: marks tests as integration tests (deselect with '-m \"not integration\"')",
    "slow: marks tests as slow",
]

[tool.ruff]
line-length = 100
target-version = "py313"
src = ["biostructbenchmark", "tests"]

[tool.ruff.lint]
select = [
    "E", "W",      # pycodestyle errors/warnings
    "F",           # pyflakes
    "I",           # isort
    "UP",          # pyupgrade
    "B",           # flake8-bugbear
    "C4",          # flake8-comprehensions
    "SIM",         # flake8-simplify
    "RUF",         # ruff-specific
    "N",           # pep8-naming
    "PTH",         # flake8-use-pathlib
    "S",           # flake8-bandit (security)
    "C90",         # mccabe complexity
    "PL",          # pylint
    "PT",          # flake8-pytest-style
    "TRY",         # tryceratops (exception handling)
    "PERF",        # perflint
    "D",           # pydocstyle (docstring conventions)
    "TCH",         # flake8-type-checking
    "T10",         # flake8-debugger (no debugger statements)
    "T20",         # flake8-print (no print in production)
    "ERA",         # eradicate (commented-out code)
    "FLY",         # flynt (f-string conversion)
    "FURB",        # refurb (modernization)
    "LOG",         # flake8-logging
    "G",           # flake8-logging-format
    "RET",         # flake8-return
    "RSE",         # flake8-raise
    "PIE",         # flake8-pie (miscellaneous)
    "INP",         # flake8-no-pep420 (implicit namespace packages)
]
ignore = [
    "E501",        # line too long (formatter handles)
    # Docstring rules - use Google convention
    "D100",        # missing docstring in public module
    "D104",        # missing docstring in public package
    "D107",        # missing docstring in __init__
    "D200",        # one-line docstring should fit on one line (overly strict)
    "D203",        # one-blank-line-before-class (conflicts with D211)
    "D205",        # blank line required between summary and description
    "D212",        # multi-line docstring summary should start at first line (Google uses D213)
    "D415",        # first line should end with punctuation (overly strict)
    # Exception handling - acceptable patterns
    "TRY003",      # long exception messages are acceptable
    "TRY203",      # re-raise without changes - acceptable for clean exception handling
    "TRY300",      # return in try block - acceptable pattern
    # Complexity - scientific code is inherently complex
    "PLR0913",     # too many arguments - scientific code often has many params
    "PLR2004",     # magic values - acceptable in scientific/numerical code
    "PLR0912",     # too many branches - complex algorithms are acceptable
    "PLR0915",     # too many statements - complex functions are acceptable
    "C901",        # too complex - scientific algorithms can be complex
    # Style preferences
    "PLC0206",     # dict iteration without .items() - acceptable for key-only iteration
    "SIM108",      # ternary operator - explicit if-else can be clearer
    "PERF401",     # list comprehension vs append - readability preference
    "RET504",      # unnecessary assignment before return - readability preference
    "G004",        # logging f-string - acceptable for simple logging
]

[tool.ruff.lint.pydocstyle]
convention = "google"

[tool.ruff.lint.per-file-ignores]
"tests/**" = ["S101", "PLR2004", "ARG001", "PLC0415", "E712", "PT009", "PT027", "RUF015", "PTH123", "B007", "RUF005", "S108", "PT011", "D", "T20", "INP001", "UP038"]
"scripts/**" = ["T20", "D103", "INP001", "PTH123", "F841"]  # Scripts use print for output and are utility code
"biostructbenchmark/__main__.py" = ["PLC0415", "PLR0915", "T20"]  # CLI entry point has conditional imports and prints

[tool.ruff.format]
quote-style = "double"
docstring-code-format = true

[tool.mypy]
python_version = "3.13"
strict = true
extra_checks = true
warn_return_any = true
warn_unused_ignores = true
show_error_codes = true
show_column_numbers = true
pretty = true
# Allow untyped calls for scientific libraries without type stubs
disallow_untyped_calls = false

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

[[tool.mypy.overrides]]
module = ["Bio.*", "numpy.*", "pandas.*"]
ignore_missing_imports = true
# BioPython has incomplete type stubs - allow broader typing
follow_imports = "skip"

[tool.coverage.run]
branch = true
source = ["biostructbenchmark"]
omit = ["tests/*"]

[tool.coverage.report]
fail_under = 80
show_missing = true
exclude_lines = [
    "pragma: no cover",
    "if TYPE_CHECKING:",
    "raise NotImplementedError",
]

[tool.bandit]
targets = ["biostructbenchmark"]
exclude_dirs = ["tests"]

[tool.interrogate]
fail-under = 80
verbose = 2
ignore-init-method = true
ignore-init-module = true
ignore-magic = true
ignore-private = true
ignore-semiprivate = false
exclude = ["tests", "docs", "build", "dist"]
color = true

[tool.vulture]
min_confidence = 80
paths = ["biostructbenchmark"]
exclude = ["tests/", ".venv/"]