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pyproject.toml
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[tool.poetry]
name = "biotrainer"
version = "0.9.6"
description = "Biotrainers for embeddings"
authors = [
"Christian Dallago <[email protected]>",
"Sebastian Franz <[email protected]>",
"Joaquin Gomez Sanchez <[email protected]>",
"Michael Heinzinger <[email protected]>"
]
license = "AFL v3.0"
readme = "README.md"
classifiers = [
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"License :: OSI Approved :: AFL License",
"Operating System :: OS Independent",
"Intended Audience :: Science/Research",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"Topic :: Scientific/Engineering :: Visualization"
]
[tool.poetry.scripts]
biotrainer = 'biotrainer.utilities.cli:main'
[tool.poetry.urls]
Issues = "https://github.com/sacdallago/biotrainer/issues"
Repository = "https://github.com/sacdallago/biotrainer"
[tool.poetry.dependencies]
python = ">=3.10,<3.12"
accelerate = "^1.1.1"
biopython = ">=1.83,<2.0"
h5py = ">=3.8.0,<4.0.0"
pip-audit = "^2.7.3"
protobuf = "^5.29.1"
numpy = "2.1.3"
"ruamel.yaml" = ">=0.17.40,<0.18.0"
sentencepiece = "^0.2.0"
scipy = "1.15.1"
scikit-learn = "^1.5.1"
tensorboard = "^2.18.0"
torch = "2.6.0"
tqdm = "^4.67.0"
transformers = "^4.48.2"
torchmetrics = "^1.5.1"
safetensors = "^0.4.4"
onnx = "1.16.1" # Latest version 1.17.0 has issues currently https://github.com/sacdallago/biotrainer/issues/111
onnxscript = "^0.1.0.dev20240806"
onnxruntime = "^1.19.0"
pandas = "^2.2.3"
datasets = "^3.1.0"
umap-learn = "^0.5.7"
[tool.poetry.group.dev.dependencies]
pytest = "^8.3.4"
build = "^1.2.2"
[build-system]
requires = ["poetry-core>=1.0.0"]
build-backend = "poetry.core.masonry.api"