pyproject.toml

# package
[build-system]
requires = ["setuptools", "setuptools-scm"]
build-backend = "setuptools.build_meta"

[project]
name = "imgx"
authors = [
    {name = "Yunguan Fu", email = "yunguan.fu.18@ucl.ac.uk"},
]
description = "A Jax-based deep learning toolkit for biomedical applications."
requires-python = ">=3.9"
license = {text = "Apache-2.0"}
version = "0.3.2"

[project.scripts]
imgx_train="imgx.run_train:main"
imgx_valid="imgx.run_valid:main"
imgx_test="imgx.run_test:main"

[tool.setuptools]
packages = ["imgx"]
package-dir = {"imgx"="./imgx"}

# pytest
[tool.pytest.ini_options]
markers = [
    "slow", # slow unit tests
    "integration", # integration tests
]

# pre-commit
[tool.isort]
py_version=39
known_third_party = ["SimpleITK","absl","chex","hydra","jax","numpy","omegaconf","optax",
    "pandas","pytest","ray","rdkit","setuptools","tensorflow","tensorflow_datasets","tree","wandb"]
multi_line_output = 3
force_grid_wrap = 0
line_length = 100
include_trailing_comma = true
use_parentheses = true

[tool.mypy]
python_version = "3.9"
warn_unused_configs = true
ignore_missing_imports = true
disable_error_code = ["misc","attr-defined","call-arg"]
show_error_codes = true
files = "**/*.py"

[tool.ruff]
line-length = 100
# Enable Pyflakes `E` and `F` codes by default.
select = [
    "F", # Pyflakes
    "E", "W", # pycodestyle
    "UP", # pyupgrade
    "N", # pep8-naming
    # flake8
    "YTT",
    "ANN",
    "S",
    "BLE",
    "B",
    "A",
    "C4",
    "T10",
    "EM",
    "ISC",
    "ICN",
    "T20",
    "PT",
    "Q",
    "RET",
    "SIM",
    "TID",
    "ARG",
    "DTZ",
    "PIE",
    "PGH", # pygrep-hooks
    "RUF", # ruff
    "PLC", "PLE", "PLR", "PLW",  # Pylint
]
ignore = [
    "ANN002", # MissingTypeArgs
    "ANN003", # MissingTypeKwargs
    "ANN101", # MissingTypeSelf
    "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
    "S301", # `pickle` and modules that wrap it can be unsafe when used to deserialize untrusted data, possible security issue
    "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
]
# Exclude a variety of commonly ignored directories.
exclude = [
    ".bzr",
    ".direnv",
    ".eggs",
    ".git",
    ".hg",
    ".mypy_cache",
    ".nox",
    ".pants.d",
    ".ruff_cache",
    ".svn",
    ".tox",
    ".venv",
    "__pypackages__",
    "_build",
    "buck-out",
    "build",
    "dist",
    "node_modules",
    "venv",
]
# Allow unused variables when underscore-prefixed.
dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
# Assume Python 3.9
target-version = "py39"

[tool.ruff.mccabe]
# Unlike Flake8, default to a complexity level of 10.
max-complexity = 10

[tool.ruff.per-file-ignores]
"test_*.py" = ["S101"]
"*_test.py" = ["S101"]

[tool.ruff.pydocstyle]
# Use Google-style docstrings.
convention = "google"

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