ProtEnc/pyproject.toml at master · jderiz/ProtEnc · GitHub

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[tool.poetry]
name = "protenc"
version = "0.1.6"
description = "Extract protein embeddings from protein language models."
authors = ["Kristian Klemon <kristian.klemon@gmail.com>"]
readme = "README.md"
packages = [{include = "protenc"}, {include = "protenc_mcp"}]
repository = "https://github.com/kklemon/ProtEnc"
homepage = "https://github.com/kklemon/ProtEnc"

[tool.poetry.scripts]
protenc = 'protenc.console.extract:entrypoint'
protenc-mcp = 'protenc_mcp.server:main'

[tool.poetry.dependencies]
python = ">=3.10,<3.13"
lmdb = ">=1.4.1"
pandas = ">=2.1.1"
tqdm = ">=4.66.1"
biopython = ">=1.81"
sentencepiece = ">=0.1.99"
json-stream = ">=2.3.2"
humanfriendly = ">=10.0"
pytest = ">=7.4.2"
sequence_models = "*"
mcp = ">=1.13,<2.0"
colorlog = ">=6.7.0"
h5py = ">=3.10.0"
transformers = ">=4.33.3"
huggingface_hub = "<0.35.0"
torch = {version = ">=2.0.1", source = "pytorch-gpu-src"}
esm = {git = "https://github.com/Biohub/esm.git", branch = "main"}
# tensordict dependency has been removed

[[tool.poetry.source]]
name = "pytorch-gpu-src"
url = "https://download.pytorch.org/whl/cu118"
priority = "explicit"


[tool.poetry.group.dev.dependencies]
ipython = "^8.16.0"

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