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pyproject.toml
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pyproject.toml
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[tool.poetry]
name = "gene-disease-prediction"
version = "1.0.0"
description = "Predicting gene-disease associations using graph neural networks"
authors = ["Balázs Glávits <balazs@glavits.hu>"]
readme = "README.md"
[[tool.poetry.source]]
name = "pytorch-cpu"
url = "https://download.pytorch.org/whl/cpu"
priority = "explicit"
[[tool.poetry.source]]
name = "pytorch-cu121"
url = "https://download.pytorch.org/whl/cu121"
priority = "explicit"
[[tool.poetry.source]]
name = "pyg-torch-2_1_0_cpu"
url = "https://data.pyg.org/whl/torch-2.1.0%2Bcpu.html"
priority = "explicit"
[[tool.poetry.source]]
name = "pyg-torch-2_1_0_cu121"
url = "https://data.pyg.org/whl/torch-2.1.0%2Bcu121.html"
priority = "explicit"
[tool.poetry.dependencies]
python = "<3.12,>=3.9"
torch-geometric = "~2.4"
lightning = "~2.0"
ogb = "~1.3"
optuna = "~3.4"
numpy = "^1.26"
scipy = "^1.11"
scikit-learn = "^1.3"
pandas = "^2.1"
polars = "^0.19"
obonet = "*"
tqdm = "*"
networkx = "*"
pyarrow = "*"
matplotlib = "*"
requests = "*"
torchinfo = "*"
botocore = "^1.31" # transitive depencency of lightning
[tool.poetry.group.cpu.dependencies]
torch = { version = "2.1.0+cpu", source = "pytorch-cpu" }
torchvision = { version = "~0.16+cpu", source = "pytorch-cpu" }
pyg-lib = { version = "~0.3+pt21cpu", source = "pyg-torch-2_1_0_cpu" }
torch-scatter = { version = "~2.1+pt21cpu", source = "pyg-torch-2_1_0_cpu" }
torch-sparse = { version = "~0.6+pt21cpu", source = "pyg-torch-2_1_0_cpu" }
torch-cluster = { version = "~1.6+pt21cpu", source = "pyg-torch-2_1_0_cpu" }
torch-spline-conv = { version = "~1.2+pt21cpu", source = "pyg-torch-2_1_0_cpu" }
# [tool.poetry.group.cuda.dependencies]
# torch = { version = "2.1.0+cu121", source = "pytorch-cu121" }
# torchvision = { version = "~0.16+cu121", source = "pytorch-cu121" }
# pyg-lib = { version = "~0.3+pt21cu121u", source = "pyg-torch-2_1_0_cu121" }
# torch-scatter = { version = "~2.1+pt21cu121", source = "pyg-torch-2_1_0_cu121" }
# torch-sparse = { version = "~0.6+pt21cu121", source = "pyg-torch-2_1_0_cu121" }
# torch-cluster = { version = "~1.6+pt21cu121", source = "pyg-torch-2_1_0_cu121" }
# torch-spline-conv = { version = "~1.2+pt21cu121", source = "pyg-torch-2_1_0_cu121" }
[tool.poetry.group.dev]
optional = true
[tool.poetry.group.dev.dependencies]
tabulate = "^0.9.0"
tensorflow-cpu = "^2.14.0"
tensorboard = "^2.14.1"
isort = "^5.12.0"
black = "^23.9.1"
mypy = "^1.5.1"
rich = "^13.6.0"
snakeviz = "^2.2.0"
lxml = "^4.9.3"
optuna-dashboard = "^0.13.0"
[tool.isort]
profile = "black"
[tool.black]
line-length = 120
[build-system]
requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api"