[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"
[project]
name = "biopython-mcp"
version = "0.1.4"
description = "Model Context Protocol server providing BioPython library capabilities for biological sequence analysis, alignment, database access, and structural bioinformatics"
readme = "README.md"
requires-python = ">=3.10"
license = {text = "MIT"}
authors = [
{name = "Maneesh KUMAR", email = "maneesh.irs@gmail.com"}
]
keywords = [
"biopython",
"mcp",
"model-context-protocol",
"bioinformatics",
"genomics",
"protein-analysis",
"sequence-alignment"
]
classifiers = [
"Development Status :: 3 - Alpha",
"Intended Audience :: Developers",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: MIT License",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"Topic :: Software Development :: Libraries :: Python Modules",
]
dependencies = [
"biopython>=1.81",
"mcp>=0.9.0",
"fastmcp>=0.2.0",
"httpx>=0.25.0",
"pydantic>=2.0.0",
]
[project.optional-dependencies]
dev = [
"pytest>=7.4.0",
"pytest-cov>=4.1.0",
"pytest-asyncio>=0.21.0",
"black>=23.7.0",
"ruff>=0.1.0",
"mypy>=1.5.0",
"pre-commit>=3.3.0",
"types-requests",
"hatchling",
]
[project.urls]
Homepage = "https://github.com/kmaneesh/biopython-mcp"
Repository = "https://github.com/kmaneesh/biopython-mcp"
Documentation = "https://github.com/kmaneesh/biopython-mcp/blob/main/docs"
Issues = "https://github.com/kmaneesh/biopython-mcp/issues"
[project.scripts]
biopython-mcp = "biopython_mcp.server:main"
[tool.hatch.build.targets.wheel]
packages = ["biopython_mcp"]
[tool.black]
line-length = 100
target-version = ["py310", "py311", "py312"]
include = '\.pyi?$'
[tool.ruff]
line-length = 100
target-version = "py310"
select = [
"E", # pycodestyle errors
"W", # pycodestyle warnings
"F", # pyflakes
"I", # isort
"B", # flake8-bugbear
"C4", # flake8-comprehensions
"UP", # pyupgrade
"ARG", # flake8-unused-arguments
"SIM", # flake8-simplify
]
ignore = [
"E501", # line too long (handled by black)
"B008", # do not perform function calls in argument defaults
"C901", # too complex
]
[tool.ruff.per-file-ignores]
"__init__.py" = ["F401"]
"tests/**/*.py" = ["ARG", "S101"]
[tool.mypy]
python_version = "3.10"
warn_return_any = true
warn_unused_configs = true
disallow_untyped_defs = true
disallow_incomplete_defs = true
check_untyped_defs = true
no_implicit_optional = true
warn_redundant_casts = true
warn_unused_ignores = true
warn_no_return = true
strict_equality = true
ignore_missing_imports = true
[tool.pytest.ini_options]
minversion = "7.0"
addopts = "-ra -q --strict-markers --cov=biopython_mcp --cov-report=term-missing"
testpaths = ["tests"]
pythonpath = ["."]
asyncio_mode = "auto"
markers = [
"network: tests that require outbound network access",
"entrez: tests that require NCBI Entrez access (requires NCBI_EMAIL and RUN_ENTREZ_TESTS=1)",
]
[tool.coverage.run]
source = ["biopython_mcp"]
omit = ["*/tests/*", "*/__pycache__/*"]
[tool.coverage.report]
exclude_lines = [
"pragma: no cover",
"def __repr__",
"raise AssertionError",
"raise NotImplementedError",
"if __name__ == .__main__.:",
"if TYPE_CHECKING:",
"@abstractmethod",
]
