pyproject.toml

[project]
name = "lbster"
readme = "README.md"
description = "Language models for Biological Sequence Transformation and Evolutionary Representation."
authors = [{name = "Nathan C. Frey", email = "frey.nathan.nf1@gene.com"}]
dynamic = ["version", "dependencies", "optional-dependencies"]
requires-python = ">=3.10"

[build-system]
requires = ["setuptools >= 65", "setuptools_scm[toml]>=6.2"]
build-backend = 'setuptools.build_meta'

[project.scripts]
lobster_train = "lobster.cmdline:train"
lobster_embed = "lobster.cmdline:embed"
lobster_predict = "lobster.cmdline:predict"
lobster_intervene = "lobster.cmdline:intervene"
lobster_intervene_multiproperty = "lobster.cmdline:intervene_multiproperty"
lobster_perplexity = "lobster.cmdline:perplexity"
lobster_eval = "lobster.cmdline:eval_embed"

[tool.setuptools.dynamic]
dependencies = {file = ["requirements.in"]}

[tool.setuptools.dynamic.optional-dependencies]
dev = {file = ["requirements-dev.in"]}
mgm = {file = ["requirements-mgm.in"]}

[tool.setuptools.packages.find]
where = ["src"]

[tool.setuptools.package-data]
lobster = ["*.txt", "*.json", "*.yaml"]
"lobster.assets" = ["**/*.txt", "**/*.json", "**/*.yaml"]
"lobster.hydra_config" = [ "**/*.yaml"]

[tool.setuptools_scm]
search_parent_directories = true
version_scheme = "no-guess-dev"
fallback_version = "0.0.0"
local_scheme = "no-local-version" # see https://github.com/pypa/setuptools-scm/issues/455

[tool.ruff]
line-length = 120
exclude = [
  "scripts",
  "notebooks",
  "src/lobster/model/openfold_utils"
]

[tool.ruff.lint]
select = [
    "E",  # pycodestyle errors
    "W",  # pycodestyle warnings
    "F",  # pyflakes
    "I",  # isort
    "B",  # flake8-bugbear
]

ignore = [
    "E501",  # line too long, handled by black
    "B008",  # do not perform function calls in argument defaults
    "B905",  # requires python >= 3.10
    "B007",  # unused-loop-control-variable
    "E741",  # ambiguous-variable-name
]

[tool.ruff.lint.per-file-ignores]
"__init__.py" = [
    "F401", # MODULE IMPORTED BUT UNUSED
]
"tests/**/*.py" = [
  "D"
]