[project]
name = 'rf_diffusion'
version = '0.0.0'
dependencies = []
requires-python = '>=3.11'

[build-system]
requires = ['hatchling']
build-backend = 'hatchling.build'

[tool.yapf]
based_on_style = 'pep8'
indent_width = 4
column_limit = 123
blank_line_before_nested_class_or_def = false
blank_lines_around_top_level_definition = 1
arithmetic_precedence_indication = true

[tool.pyright]
include = [
	"rf_diffusion", 
	"lib/rf2aa/rf2aa", 
	"lib/cifutil/cifutils", 
	"lib/datahub/datahub",
	"lib/rf2aa/lib/ipd/ipd", 
	]
exclude = [
    "**/__pycache__",
]
defineConstant = { DEBUG = true }
typeCheckingMode = "standard"
reportMissingImports = true
reportMissingTypeStubs = false
pythonPlatform = "Linux"
requires-python = ">=3.11"
pythonVersion = "3.12"

[tool.docformatter]
recursive = true
wrap-summaries = 88
wrap-descriptions = 88
blank = true
style = 'sphinx'

[tool.ruff]
lint.ignore = [
   'E731', #  [ ] Do not assign a `lambda` expression, use a `def`
   'E402', #  [ ] Module level import not at top of file
   'E741', #  [ ] Ambiguous variable name: `I`
   'E701', #  [ ] Multiple statements on one line (colon)
   'F403', #  [ ] `from Attention_module import *` used; unable to detect undefined names
   'F821', #  [ ] Undefined name `AND`
   'F405'
]
lint.dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?)|ic)$"
line-length = 123
target-version = "py39"
format.quote-style = "single"
format.indent-style = "space"
format.docstring-code-format = true
exclude = [
    ".bzr",
    ".direnv",
    ".eggs",
    ".git",
    ".git-rewrite",
    ".hg",
    ".ipynb",
    ".ipynb_checkpoints",
    ".mypy_cache",
    ".nox",
    ".pants.d",
    ".pyenv",
    ".pytest_cache",
    ".pytype",
    ".ruff_cache",
    ".svn",
    ".tox",
    ".venv",
    ".vscode",
    "__pypackages__",
    "_build",
    "buck-out",
    "build",
    "dist",
    "node_modules",
    "site-packages",
    "venv",
   "images",
   "lib",
   "openfold",
   "pymol_config",
   "README.md",
   "fused_mpnn",
   "se3_flow_matching",
]


[tool.pytest.ini_options]
minversion = 6.0
addopts = '--disable-warnings -q -m "not nondeterministic and not ci"'
pythonpath = ['.', 'rf_diffusion', 'rf2aa/SE3Transformer']
testpaths = ['rf_diffusion/test_*.py', 'rf_diffusion/tests', 'ipd']
markers = [
    'slow: marks tests as slow (deselect with -m "not slow")',
    'fast: tests that run in a second or two',
    'noparallel: tests teat cant run in parallel',
    "ci: tests that should only run in ci",
   ]