pyproject.toml

[tool.isort]
profile = "black"
py_version = 39
multi_line_output = 3  # How imports are formatted when they span multiple lines
include_trailing_comma = true
use_parentheses = true
line_length = 88

[tool.mypy]
python_version = 3.9
namespace_packages = true
incremental = false
warn_redundant_casts = true
#warn_return_any = true
warn_unused_configs = true
warn_unused_ignores = true  # Flag unneeded type ignore statements
allow_redefinition = true
disallow_untyped_calls = true
disallow_untyped_defs = true
disallow_incomplete_defs = true
check_untyped_defs = true
disallow_untyped_decorators = false  # Allow decorators that convert a typed function into an untyped one
strict_optional = true
strict_equality = true
explicit_package_bases = true
follow_imports = "skip"
exclude = ["ProteinMPNN/", "openfold/", "build/"]


[[tool.mypy.overrides]]
module = [
    "Bio.*",
    "setuptools.*",
    "pandas.*",
    "omegaconf.*",
    "hydra.*",
    "absl.*",
    "neptune.*",
    "scipy.*",
    "tree.*",
    "biotite.*",
    "GPUtil.*",
    "esm.*",
    "mdtraj.*",
    "tmtools.*",
    "matplotlib.*",
    "sklearn.*",
    "anarci.*",
    "s3fs.*",
    "seaborn.*"
]
ignore_missing_imports = true

[tool.ruff]
target-version = "py39"  # Assume Python 3.9
select = [  # Enable a wide range of existing codes.
    "F", # Pyflakes
    "E", "W", # pycodestyle
    "UP", # pyupgrade
    "N", # pep8-naming
    "YTT", "ANN", "S", "BLE", "B", "A", "C4", "T10", "EM", "ISC", "ICN", "T20", "PT", "Q", "RET", "SIM", "TID", "ARG", "DTZ", "PIE", # flake8
    "PGH", # pygrep-hooks
    "RUF", # ruff
    "PLC", "PLE", "PLR", "PLW", # pylint
]
ignore = [
    "ANN002", # MissingTypeArgs
    "ANN003", # MissingTypeKwargs
    "ANN101", # MissingTypeSelf
    "ANN102", # MissingTypeCls
    "ANN401", # Avoid "Dynamically typed expressions (typing.Any) are disallowed"
    "EM101", # Exception must not use a string literal, assign to variable first
    "EM102", # Exception must not use an f-string literal, assign to variable first
    "RET504", # Unnecessary variable assignment before `return` statement
    "PLR0913", # Too many arguments to function call
    "PLR0915", # Too many statements
    "PLE0605", # Invalid format for `__all__`, must be `tuple` or `list`
    "PLR0912", # Too many branches
    "S113", # Avoid "Probable use of requests call without timeout"
    "DTZ005", # Avoid requiring timezone to be specified in datetime.datetime.now()
]

[tool.ruff.per-file-ignores]
"test_*.py" = [
    "S101",  # Using `assert` is fine in test files
    "PLR2004"  # Using constant without defining a variable is fine in test files
]
"framedipt/data/parsers.py" = [
    "SIM115",  # Use context handler for opening files
    "PLW2901",  # for loop variable overwritten by assignment target
    "N806"  # Variable in function should be lowercase
]
"framedipt/data/transforms.py" = [
    "N806",  # Variable in function should be lowercase
    "N802",  # Function name should be lowercase
    "N803",  # Argument name should be lowercase
    "PLR2004",  # Magic value used in comparison
    "S101",  # Use of `assert`
]

[tool.ruff.pydocstyle]
convention = "google"  # Follow the Google Style Guide

[tool.ruff.pylint]
allow-magic-value-types = ["int", "str"]