AFDB-Integration-Kit/pyproject.toml at main · PDBeurope/AFDB-Integration-Kit · GitHub

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[project]
name = "afdb-toolkit"
version = "0.1.2"
description = "A comprehensive toolkit for integrating structural models into the AlphaFold Database (AFDB)."
readme = "README.md"
requires-python = ">=3.12"
dependencies = [
    "gemmi>=0.7.3",
    "gemmi-program>=0.7.3",
    "jsonschema>=4.24.0",
    "numpy>=2.3.1",
    "pyarrow>=23.0.1",
    "duckdb>=1.1.3",
    "tqdm>=4.66.5",
    "requests>=2.33.0",
    "typer>=0.16.0",
    "orjson>=3.11.6",
]

[project.optional-dependencies]
# Production pipeline dependencies (clash detection, interface residues)
# Note: torch_cluster must be installed separately - see README for instructions
production = [
    "biotite>=1.0.0",
    "pydssp>=0.9.0",
    "torch>=2.12.0",
    "fastpdb>=1.2",
]

[project.scripts]
afdb-uniprot-shard = "uniprot.scripts.shard_uniprot:main"
afdb-uniprot-extract = "uniprot.scripts.extract_subset:main"
afdb-uniprot-merge = "uniprot.scripts.merge_parquet_shards:main"
afdb-uniprot-build-db = "uniprot.scripts.build_duckdb:main"
afdb-uniprot-export-model = "uniprot.scripts.export_model_metadata:main"
afdb-uniprot-export-chain = "uniprot.scripts.export_chain_metadata:main"
afdb-uniprot-combine = "uniprot.scripts.combine_metadata:main"
afdb-colabfold-convert = "afdb_integration_kit.colabfold.converter:main"

[tool.setuptools.package-data]
"afdb_integration_kit.validation" = ["defaults.yaml"]

[tool.setuptools.packages.find]
include = ["afdb_integration_kit*", "uniprot*"]
exclude = [
  "tests*",
  "examples*",
  "resources*",
  "workflow*",
  "dssp*",
  "test_examples*",
]

[dependency-groups]
dev = [
    "coverage>=7.9.2",
    "flake8>=7.3.0",
    "pre-commit>=4.2.0",
    "pytest>=9.0.3",
]
docs = [
    "furo>=2024.8.6",
    "sphinx>=8.2.3",
    "sphinx-autodoc-typehints>=3.2.0",
]