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pyproject.toml
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pyproject.toml
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[build-system]
requires = ["setuptools"]
build-backend = "setuptools.build_meta"
[project]
name = "proteinflow"
version = "2.8.0"
authors = [
{name = "Liza Kozlova", email = "liza@adaptyvbio.com"},
]
description = "Versatile pipeline for processing protein structure data for deep learning applications."
readme = "README.md"
requires-python = ">=3.8"
license = {text = "BSD-3-Clause"}
dependencies = [
"numpy>=1.21,<1.25",
"editdistance>=0.6.0",
"Biopython==1.79",
"click>=8.1.3",
"biopandas>=0.4.1",
"boto3",
"p_tqdm>=1.4.0",
"networkx==2.8.8", # for partitioning
"einops>=0.6.0",
"pandas>=1.5.2",
"torch>=1.10.0",
"biotite==0.35.0",
"aiobotocore",
"awscli",
"bs4>=0.0.1",
"pyyaml>=6",
"rcsbsearch",
"pre-commit",
"rdkit",
"pypdb",
"joblib",
]
keywords = ["bioinformatics", "dataset", "protein", "PDB", "deep learning", "antibody"]
[project.scripts]
proteinflow = "proteinflow.cli:cli"
[project.optional-dependencies]
processing = [
"py3Dmol",
"methodtools",
"tmtools",
"fair-esm",
"MDAnalysis",
"ablang",
"igfold",
"immunebuilder",
"blosum>=2.0",
]
[tool.setuptools.packages]
find = {}
[tool.pydocstyle]
convention = "numpy"
[tool.docsig]
disable = [
"E109",
]
ignore-no-parameters = true