Paper2AgentBench/pyproject.toml at main · joed3/Paper2AgentBench · GitHub

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[build-system]
requires = ["setuptools>=45", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "alphagenome-mcp"
version = "1.0.0"
description = "Model Context Protocol (MCP) server for AlphaGenome - Google DeepMind's genomic prediction model"
readme = "README.md"
requires-python = ">=3.10"
license = { file = "LICENSE" }
authors = [
    { name = "AlphaGenome MCP Contributors" }
]
keywords = [
    "genomics",
    "machine learning",
    "mcp",
    "alphagenome",
    "bioinformatics",
    "variant analysis"
]
classifiers = [
    "Development Status :: 4 - Beta",
    "Environment :: Console",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: Apache Software License",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Topic :: Scientific/Engineering :: Artificial Intelligence",
    "Topic :: Scientific/Engineering :: Bio-Informatics"
]

dependencies = [
    # Core AlphaGenome dependencies
    "alphagenome",
    "absl-py",
    "anndata",
    "grpcio>=1.67.1",
    "immutabledict",
    "intervaltree",
    "jaxtyping",
    "matplotlib",
    "ml_dtypes",
    "numpy",
    "pandas",
    "protobuf>=5.28.3",
    "pyarrow",
    "scipy",
    "seaborn",
    "tqdm",
    "typeguard",
    "typing_extensions",
    "zstandard",

    # MCP and server dependencies
    "fastmcp>=0.1.0",
    "uvicorn>=0.20.0",
    "uv>=0.8.13",

    # Visualization dependencies
    "plotnine>=0.12.0",

    # Additional dependencies for tools
    "ipython",
    "jupyter",
]

[project.optional-dependencies]
dev = [
    "pytest>=7.0.0",
    "pytest-asyncio>=0.21.0",
    "pytest-cov>=4.0.0",
    "black>=23.0.0",
    "isort>=5.12.0",
    "mypy>=1.0.0",
    "ruff>=0.1.0",
]

test = [
    "pytest>=7.0.0",
    "pytest-asyncio>=0.21.0",
    "pytest-cov>=4.0.0",
]

docs = [
    "sphinx>=5.0",
    "sphinx-autodoc-typehints",
    "sphinx-book-theme",
    "myst-nb",
]

[project.scripts]
alphagenome-mcp = "src.alphagenome_mcp:main"

[project.urls]
Homepage = "https://github.com/your-org/alphagenome-mcp"
Documentation = "https://alphagenome-mcp.readthedocs.io"
Repository = "https://github.com/your-org/alphagenome-mcp"
"Bug Tracker" = "https://github.com/your-org/alphagenome-mcp/issues"
"AlphaGenome Docs" = "https://www.alphagenomedocs.com/"

[tool.setuptools.packages.find]
where = ["."]

[tool.setuptools.package-data]
"*" = ["*.json", "*.yaml", "*.yml", "*.csv", "*.tsv"]

[tool.pytest.ini_options]
testpaths = ["tests"]
python_files = ["*_test.py", "test_*.py"]
python_classes = ["Test*"]
python_functions = ["test_*"]
addopts = [
    "-v",
    "--tb=short",
    "--strict-markers",
    "--cov=src",
    "--cov-report=term-missing",
]

[tool.black]
line-length = 100
target-version = ["py310", "py311", "py312"]

[tool.isort]
profile = "black"
line_length = 100

[tool.mypy]
python_version = "3.10"
warn_return_any = true
warn_unused_configs = true
ignore_missing_imports = true

[tool.ruff]
line-length = 100
target-version = "py310"
select = ["E", "F", "W", "I", "N", "B", "UP"]
ignore = ["E501"]  # Line too long - handled by black

[tool.coverage.run]
branch = true
source = ["src"]

[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",
    "def __repr__",
    "if __name__ == .__main__.:",
    "raise NotImplementedError",
    "if TYPE_CHECKING:",
]