pyproject.toml

[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[project]
name = "mavedb-link"
version = "0.5.7"
description = "MCP/API server that grounds variant-effect work in MaveDB (multiplexed assays of variant effect)"
readme = "README.md"
license = { text = "MIT" }
authors = [
    { name = "mavedb-link contributors", email = "bernt.popp@charite.de" },
]
keywords = [
    "mavedb", "mave", "variant-effect", "deep-mutational-scanning", "mcp",
    "api", "bioinformatics", "functional-assay", "score-set",
]
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Programming Language :: Python :: 3.14",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Typing :: Typed",
]
requires-python = ">=3.12"
dependencies = [
    "fastapi>=0.115.0,<1.0.0",
    "uvicorn[standard]>=0.52.3,<1.0.0",
    "pydantic>=2.13.5,<3.0.0",
    "pydantic-settings>=2.15.0,<3.0.0",
    "httpx>=0.28.0,<1.0.0",
    "structlog>=24.4.0,<27.0.0",
    "orjson>=3.12.0,<4.0.0",
    "rich>=13.0.0,<16.0.0",
    "typer>=0.27.2,<1.0.0",
    "mcp[cli]>=1.27.0,<2.0.0",
    "fastmcp>=3.4.7,<4.0.0",
    "zstandard>=0.22.0,<1.0.0",
]

[dependency-groups]
dev = [
    "pytest>=8.3.0,<10.0.0",
    "pytest-asyncio>=0.24.0,<2.0.0",
    "pytest-cov>=5.0.0,<8.0.0",
    "pytest-mock>=3.14.0,<4.0.0",
    "pytest-xdist>=3.6.0,<4.0.0",
    "respx>=0.21.0,<1.0.0",
    "ruff>=0.16.8,<1.0.0",
    "mypy>=2.3.1,<3.0.0",
]

[project.urls]
Homepage = "https://github.com/berntpopp/mavedb-link"
Repository = "https://github.com/berntpopp/mavedb-link"
"Bug Tracker" = "https://github.com/berntpopp/mavedb-link/issues"

[project.scripts]
mavedb-link = "server:main"
mavedb-link-mcp = "mcp_server:main"
mavedb-link-data = "mavedb_link.ingest.cli:main"
mavedb-link-cache = "mavedb_link.data.cache_cli:main"

[tool.hatch.build.targets.wheel]
packages = ["mavedb_link"]
include = ["server.py", "mcp_server.py"]
artifacts = ["mavedb_link/data/*.sql"]

[tool.ruff]
line-length = 100
target-version = "py312"

[tool.ruff.lint]
# `select`, not `extend-select`: ruff 0.16 grew its *implicit* default rule set from
# 59 to 413 rules, so `extend-select` would silently inherit ~350 unopted rules. This
# list is already a superset of the pre-0.16 default (E4/E7/E9 + F), so the effective
# policy is byte-identical -- it is now pinned instead of inherited.
select = [
    "E", "W", "F", "I", "N", "UP", "B", "C4", "S", "T20", "SIM", "RUF",
]
ignore = [
    "E501",   # Line too long (handled by formatter)
    "B008",   # FastAPI Query/Depends pattern
    "S101",   # asserts ok in tests (also per-file-ignores)
    "N812",   # single-letter module aliases
]

[tool.ruff.format]
quote-style = "double"
indent-style = "space"
line-ending = "lf"

[tool.ruff.lint.per-file-ignores]
"tests/**/*" = ["S101", "S104", "S105", "S106", "S110", "T20", "B011", "SIM105", "SIM108"]
"mcp_server.py" = ["T20"]
"scripts/**/*" = ["T20"]

[tool.ruff.lint.pydocstyle]
convention = "google"

[tool.mypy]
python_version = "3.12"
strict = true
warn_return_any = true
warn_unused_configs = true
disallow_untyped_defs = true
no_implicit_optional = true
warn_redundant_casts = true
warn_unused_ignores = true
warn_no_return = true
warn_unreachable = true
exclude = [
    ".*site-packages.*",
    ".*/\\.venv/.*",
    "htmlcov/.*",
]

[[tool.mypy.overrides]]
module = [
    "structlog.*",
    "mcp.*",
    "fastmcp.*",
    "fastapi.*",
    "pydantic.*",
    "pydantic_settings.*",
    "httpx.*",
    "uvicorn.*",
]
ignore_missing_imports = true

[tool.pytest.ini_options]
minversion = "8.0"
addopts = [
    "--strict-markers",
    "--strict-config",
    "-ra",
]
testpaths = ["tests"]
asyncio_mode = "auto"
asyncio_default_fixture_loop_scope = "function"
markers = [
    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
    "integration: marks tests that hit the live MaveDB API",
    "unit: marks tests as unit tests",
    "mcp: marks tests that test MCP functionality",
]

[tool.coverage.run]
source = ["mavedb_link"]
omit = ["tests/*", "*/.venv/*"]

[tool.coverage.report]
fail_under = 80
exclude_lines = [
    "pragma: no cover",
    "def __repr__",
    "raise NotImplementedError",
    "if __name__ == .__main__.:",
    "if TYPE_CHECKING:",
    "class .*\\bProtocol\\):",
    "@(abc\\.)?abstractmethod",
]
show_missing = true

[tool.coverage.html]
directory = "htmlcov"