ExprDecay/pyproject.toml at main · turgaybulut/ExprDecay · GitHub

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[project]
name = "exprdecay"
version = "0.1.0"
description = "ExprDecay code for gene-level relative mRNA-stability prediction."
readme = "README.md"
requires-python = ">=3.11"
dependencies = [
    "h5py>=3.16.0",
    "joblib>=1.5.0",
    "lightgbm>=4.6.0",
    "numpy>=2.4.6",
    "pandas>=3.0.3",
    "pyarrow>=22.0.0",
    "remotezip>=0.12.3",
    "scikit-learn>=1.9.0",
    "scipy>=1.17.1",
]

[project.optional-dependencies]
saluki = [
    "genomekit==7.5.0",
    "torch==2.13.0",
]
foundation = [
    "torch==2.13.0",
    "transformers>=4.44,<5",
]

[project.scripts]
exprdecay = "exprdecay.cli:main"

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

[dependency-groups]
dev = [
    "basedpyright>=1.39.8",
    "ruff>=0.15.17",
]

[tool.uv]
package = true

[tool.hatch.build.targets.wheel]
packages = ["src/exprdecay"]

[tool.ruff]
target-version = "py311"
line-length = 120
src = ["src"]
extend-exclude = [
    "results",
    "data",
    "checkpoints",
    "runs",
]

[tool.ruff.lint]
select = [
    "E",
    "F",
    "I",
    "UP",
    "B",
    "SIM",
    "C4",
    "NPY",
    "PD",
    "RUF",
]
ignore = [
    "NPY002",
]

[tool.ruff.format]
quote-style = "double"
indent-style = "space"
line-ending = "lf"

[tool.basedpyright]
pythonVersion = "3.11"
typeCheckingMode = "standard"
include = ["src"]
exclude = [
    "data",
    "results",
    "checkpoints",
    "runs",
    "**/__pycache__",
]
executionEnvironments = [
    { root = "src" },
]
reportMissingTypeStubs = false
reportUnknownMemberType = false
reportUnknownArgumentType = false
reportUnknownVariableType = false
reportUnknownLambdaType = false
reportAny = false
reportArgumentType = false
reportAttributeAccessIssue = false
reportCallIssue = false
reportIndexIssue = false
reportGeneralTypeIssues = false
reportOperatorIssue = false