ImmunotherapyPredictionRNAseq/pyproject.toml at main · LuJoHae/ImmunotherapyPredictionRNAseq · GitHub

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[project]
name = "immunotherapypredictionrnaseq"
version = "0.1.0"
description = ""
authors = [
    {name = "Lukas Jonathan Haeuser", email = "lhaeuser@ethz.ch"}
]
readme = "README.md"

[tool.poetry.dependencies]
python = ">=3.12,<3.13"
# torch = { version = "2.9.1+cu130", source = "pytorch" }
datalair = {git = "https://github.com/LuJoHae/datalair.git"}
tcga = {git = "https://github.com/LuJoHae/TCGA.git"}
icir = {git = "https://github.com/LuJoHae/ICI-response.git"}
anndata = "^0.12.6"
notebook = "^7.4.7"
scikit-learn = "^1.7.2"
matplotlib = "^3.10.7"
openpyxl = "^3.1.5"
umap-learn = "^0.5.9.post2"
duckdb = "^1.4.2"
seaborn = "^0.13.2"
python-dotenv = "^1.2.1"
torch = "^2.9.1"
numpy = "1.26"
pydantic = "^2.12.5"
scanpy = "^1.11.5"
optuna = "^4.6.0"

[[tool.poetry.source]]
name = "pytorch"
url = "https://download.pytorch.org/whl/cu130"
priority = "explicit"

[build-system]
requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api"

[dependency-groups]
dev = [
    "pytest (>=9.0.1,<10.0.0)",
    "pytest-cov (>=7.0.0,<8.0.0)",
    "mypy (>=1.18.2,<2.0.0)",
    "pandas-stubs (>=2.3.2.250926,<3.0.0.0)",
    "ruff (>=0.14.6,<0.15.0)"
]
jupyter = [
    "jupyter (>=1.1.1,<2.0.0)",
    "notebook (>=7.4.7,<8.0.0)",
    "ipykernel (>=7.1.0,<8.0.0)"
]

[tool.ruff]
line-length = 88
target-version = "py311"

select = [
    "E", "F", "W",
    "I",
    "B",
    "UP",
    "C90",
    "N",
    "ANN",
    "D",
]

extend-select = [
    "RUF100", # unused noqa
]

[tool.pytest.ini_options]
markers = [
    "slow: marks tests as slow",
]
testpaths = ["tests"]