File size: 3,035 Bytes
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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"
]
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