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pyproject.toml
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pyproject.toml
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[project]
name = "lbster"
description = "Language models for Biological Sequence Transformation and Evolutionary Representation."
authors = [{name = "Nathan C. Frey", email = "[email protected]"}]
dynamic = ["version", "readme", "dependencies", "optional-dependencies"]
requires-python = ">=3.10"
[project.scripts]
lobster_train = "lobster.cmdline:train"
lobster_embed = "lobster.cmdline:embed"
lobster_predict = "lobster.cmdline:predict"
[tool.setuptools.dynamic]
dependencies = {file = ["requirements.in"]}
readme = {file = "README.md"}
[tool.setuptools.dynamic.optional-dependencies]
dev = {file = ["requirements-dev.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.mypy]
show_error_codes = true
warn_unused_ignores = true
# disallow_any_unimported = true
# check_untyped_defs = true
no_implicit_optional = true
# warn_return_any = true
# disallow_untyped_defs = true
warn_redundant_casts = true
strict_equality = true
warn_unreachable = true
plugins = ["numpy.typing.mypy_plugin"]
[[tool.mypy.overrides]]
module = [
"Bio.*",
"edlib.*",
"matplotlib.*",
"pandas.*",
"pyarrow.*",
"scipy.*",
"seaborn",
"sklearn.*",
"tqdm.*",
"transformers.*",
"rdkit.*",
"prescient.*",
"smart_open.*",
"anarci.*",
"pymol.*",
"yeji.*",
"prescient.*",
"prescient_plm.*",
]
[tool.ruff]
lint.select = [
"E", # pycodestyle errors
"W", # pycodestyle warnings
"F", # pyflakes
"I", # isort
"B", # flake8-bugbear
]
lint.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
]
exclude = [
"src/lobster/model/openfold_utils",
"tests"
]
[tool.ruff.lint.per-file-ignores]
"__init__.py" = [
"F401", # MODULE IMPORTED BUT UNUSED
]
[build-system]
requires = ["setuptools >= 65", "setuptools_scm[toml]>=6.2"]
build-backend = 'setuptools.build_meta'
[tool.setuptools_scm]
search_parent_directories = true
version_scheme = "no-guess-dev"
local_scheme = "node-and-date"
fallback_version = "0.0.0"
[tool.pycln]
all = true
disable-all-dunder-policy = true
[tool.black]
line-length = 100
[tool.isort]
line_length = 100
multi_line_output = 3
include_trailing_comma = true
force_grid_wrap = 0
use_parentheses = true
ensure_newline_before_comments = true
known_third_party=["wandb"]