[build-system]
requires = ["setuptools>=61.0", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "biomni"
dynamic = ["version"]
description = "Biomni"
readme = "README.md"
license = "Apache-2.0"
license-files = ["LICENSE"]
authors = [
    {name = "Biomni Team", email = "kexinh@cs.stanford.edu"}
]
requires-python = ">=3.11"
dependencies = ["pydantic", "langchain", "python-dotenv"]

[project.urls]
Homepage = "https://github.com/snap-stanford/biomni"
Repository = "https://github.com/snap-stanford/biomni"

[project.optional-dependencies]
gradio = ["gradio>=5.0,<6.0"]

[tool.setuptools]
include-package-data = true

[tool.setuptools.dynamic]
version = {attr = "biomni.version.__version__"}

[tool.setuptools.packages.find]
exclude = ["test*", "tutorials*"]

[tool.ruff]
src = ["src"]
line-length = 120

[tool.ruff.format]
docstring-code-format = true

[tool.ruff.lint]
select = [
    "F",      # Errors detected by Pyflakes
    "E",      # Error detected by Pycodestyle
    "W",      # Warning detected by Pycodestyle
    "I",      # isort
    #"D",      # pydocstyle
    "B",      # flake8-bugbear
    "TID",    # flake8-tidy-imports
    "C4",     # flake8-comprehensions
    "BLE",    # flake8-blind-except
    "UP",     # pyupgrade
    "RUF100", # Report unused noqa directives
    "TCH",    # Typing imports
    #"NPY",    # Numpy specific rules
    #"PTH",    # Use pathlib
    #"PL"      # pylint
]
ignore = [
    # line too long -> we accept long comment lines; black gets rid of long code lines
    "E501",
    # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
    "E731",
    # allow I, O, l as variable names -> I is the identity matrix
    "E741",
    # Missing docstring in public package
    "D104",
    # Missing docstring in public module
    "D100",
    # Missing docstring in __init__
    "D107",
    # Errors from function calls in argument defaults. These are fine when the result is immutable.
    "B008",
    # __magic__ methods are are often self-explanatory, allow missing docstrings
    "D105",
    # first line should end with a period [Bug: doesn't work with single-line docstrings]
    "D400",
    # First line should be in imperative mood; try rephrasing
    "D401",
    ## Disable one in each pair of mutually incompatible rules
    # We don’t want a blank line before a class docstring
    "D203",
    # We want docstrings to start immediately after the opening triple quote
    "D213",
    # camcelcase imported as lowercase
    "N813",
    # module import not at top level of file
    "E402",
    # Too many arguments in function definition
    "PLR0913",
    # Too many branches
    "PLR0912",
    # magic value used in comparison
    "PLR2004",
    # Too many statements
    "PLR0915",
    # Extracting value from dictionary without calling `.items()` - clashes with sim
    "PLC0206",
    # import should be at top of file
    "PLC0415",
    # do not catch blind exception
    "BLE001",
    # strip with multi characters
    "B005"
]