pyproject.toml

[tool.pytest.ini_options]
addopts = "--cov=reduce_binary" # CHANGE (name of the importing module name)
testpaths = ["tests"]

[tool.ruff]
src = ["python/src"]  # for ruff isort
namespace-packages = ["tools", "scripts", "tests"]  # for INP rule, suppress on these directories

[tool.ruff.lint]
# OPTIONALLY ADD MORE LATER
select = [
  # flake8
  "E",
  "F",
  "W",
  "B",    # Bugbear
  "D",    # Docstring
  "D213", # Multi-line docstring summary should start at the second line (replace D212)
  "N",    # Naming
  "C4",   # flake8-comprehensions
  "UP",   # pyupgrade
  "SIM",  # simplify
  "RUF",  # ruff-specific
  "RET501",  # return
  "RET502",  # return
  "RET503",  # return
  "PTH",  # path
  "NPY",  # numpy
  "PD",   # pandas
  "PYI",  # type stubs for pyright/pylance
  "PT",   # pytest
  "PIE",  #
  "LOG",  # logging
  "COM818",  # comma misplaced
  "COM819",  # comma
  "DTZ",  # datetime
  "YTT",
  "ASYNC",
  "FBT",  # boolean trap
  "A",    # Shadowing python builtins
  "EXE",  # executable (shebang)
  "FA",   # future annotations
  "ISC",  # Implicit string concatenation
  "ICN",  # Import convention 
  "INP",  # Implicit namespace package (no __init__.py)
  "Q",    # Quotes
  "RSE",  # raise
  "SLOT", # __slots__
  "PL",   # Pylint
  "TRY",  # try
  "FAST", # FastAPI
  "AIR",  # airflow
  "DOC",  # docstring

  # Not important
  "T10",  # debug statements
  "T20",  # print statements
]

ignore = [
  "E402",    # Module level import not at top of file
  "W293",    # Blank line contains whitespace
  "W291",    # Trailing whitespace
  "D10",     # Missing docstring in public module / function / etc.
  "D200",    # One-line docstring should fit on one line with quotes
  "D212",    # Multi-line docstring summary should start at the first line
  "D417",    # require documentation for every function parameter.
  "D401",    # require an imperative mood for all docstrings.
  "DOC201",  # missing Return field in docstring
  "PTH123",  # Path.open should be used instead of built-in open
  "PT006",   # Pytest parameterize style
  "N812",    # Lowercase `functional` imported as non-lowercase `F` (import torch.nn.functional as F)
  "NPY002",  # legacy numpy random
  "UP017",   # datetime.timezone.utc -> datetime.UTC
  "SIM108",  # use ternary operator instead of if-else
  "TRY003",  # long message in except
]

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

[tool.ruff.lint.pycodestyle]
# Black or ruff will enforce line length to be 88, except for docstrings and comments.
# We set it to 120 so we have more space for docstrings and comments.
max-line-length = 120

[tool.ruff.lint.isort]
# combine-as-imports = true
known-third-party = ["wandb"]
known-first-party = [
  "rust_graph",
  "bio_data_to_db",
  "apbs_binary",
  "slack_helpers",
  "biotest",
]

## Uncomment this if you want to use Python < 3.10
# required-imports = [
#   "from __future__ import annotations",
# ]

[tool.ruff.lint.flake8-tidy-imports]
# Ban certain modules from being imported at module level, instead requiring
# that they're imported lazily (e.g., within a function definition, if TYPE_CHECKING, etc.)
# NOTE: Ruff code TID is currently disabled, so this settings doesn't do anything.
banned-module-level-imports = ["torch", "tensorflow"]

[tool.ruff.lint.pylint]
max-args = 10
max-bool-expr = 10
max-statements = 100

[tool.pyright]
include = ["python/src"]

typeCheckingMode = "standard"
useLibraryCodeForTypes = true
autoImportCompletions = true