[project]
name = "plant-genomics-mcp"
version = "1.21.0"
description = "Plant genomics MCP — 50 tools across 23 live backends (Ensembl Plants, Phytozome, UniProt, Europe PMC, QuickGO, Planteome, PlantCyc/PMN, g:Profiler, AlphaFold, PDBe, InterPro, JASPAR, ThaleMine, PANTHER, OrthoDB, AraGWAS, 1001 Genomes, BLAST, Gramene, KEGG, STRING, ATTED-II, BAR) for Claude Code"
readme = "README.md"
license = { text = "MIT" }
authors = [{ name = "Jaret Arnold", email = "mjarnold1998@gmail.com" }]
requires-python = ">=3.11"
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Programming Language :: Python :: 3.14",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]
dependencies = [
    # Floor is the version the suite actually runs against. It MOVED to 2.x
    # (rather than widening) when server.py migrated off the removed
    # @server.list_tools() decorator family onto Server(on_list_tools=...):
    # that code cannot run on 1.x at all, because ServerRequestContext does
    # not exist there and the import fails outright. Leaving the old >=1.28.1
    # floor in place would let a resolver pick a version this package can no
    # longer import. The upper bound stays deliberate — a major SDK bump gets
    # opted into, not inherited silently by everyone who installs us.
    "mcp>=2,<3",
    "httpx>=0.27",
    "pydantic>=2.6",
    "starlette>=0.36",
    "uvicorn>=0.27",
    "defusedxml>=0.7",
]

[project.urls]
Homepage = "https://github.com/musharna/plant-genomics-mcp"
Changelog = "https://github.com/musharna/plant-genomics-mcp/blob/main/CHANGELOG.md"
Issues = "https://github.com/musharna/plant-genomics-mcp/issues"

[project.optional-dependencies]
dev = [
    "pytest>=8.0",
    "pytest-asyncio>=0.23",
    "pytest-httpx>=0.30",
    "pytest-cov>=5.0",
    "ruff>=0.3",
    "mypy>=1.8",
]

[project.scripts]
plant-genomics-mcp = "plant_genomics_mcp.server:main"
plant-genomics-mcp-http = "plant_genomics_mcp.server_http:main"

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

[tool.hatch.build.targets.wheel]
packages = ["src/plant_genomics_mcp"]

[tool.pytest.ini_options]
testpaths = ["tests"]
asyncio_mode = "auto"

[tool.coverage.report]
# Coverage floor (audit P8). Measured TOTAL was 94% after the v1.6.0 dispatch/
# batch/progress/consensus test backfill; 92 leaves ~2pts of slack while
# failing the build if an untested dispatch arm or a deleted test regresses it.
# pytest-cov honors fail_under from here, so `pytest --cov` fails below the
# floor. The __main__/entrypoint block (server._serve/main) is the bulk of the
# remaining gap and is intentionally not exercised in CI.
fail_under = 92
show_missing = true

[tool.ruff]
line-length = 100
target-version = "py311"

[tool.ruff.lint]
# E/F (default) plus import-sorting, bugbear, pyupgrade, and simplify.
# E501 (line-too-long) is intentionally left to the formatter — `ruff format`
# owns line-length, and a lint error on top of it is noise.
select = ["E", "F", "I", "B", "UP", "SIM"]
ignore = ["E501"]

[tool.ruff.lint.per-file-ignores]
# Nested `async with` (stdio_client + ClientSession) reads clearer than a
# combined context manager in the MCP stdio integration tests.
"tests/**" = ["SIM117"]

[tool.mypy]
python_version = "3.11"
ignore_missing_imports = true
warn_unused_ignores = true

[tool.mutmut]
source_paths = ["src"]
also_copy = [".dockerignore", ".editorconfig", ".github", ".gitignore", ".mcp.json", ".pre-commit-config.yaml", ".zenodo.json", "CHANGELOG.md", "CITATION.cff", "CLAUDE.md", "CODE_OF_CONDUCT.md", "CONTRIBUTING.md", "Dockerfile", "Dockerfile.http", "LICENSE", "README.md", "REGISTRIES.md", "SECURITY.md", "assets", "docs", "examples", "glama.json", "scripts", "server.json", "smithery.yaml"]
# a module-level asyncio.Semaphore binds to the first event loop, which under the in-process mutmut runner is not the test loop
pytest_add_cli_args = ["--deselect", "tests/test_blast.py::test_blast_semaphore_caps_concurrent_at_two"]