[project]
name = "breedsim-mcp"
version = "0.4.2"
description = "MCP server for breeding-scheme simulation — returns distributions, never a single stochastic run"
readme = "README.md"
# GPL, not MIT. AlphaSimR itself is MIT, but rpy2 is GPLv2+ and we import it
# directly, so the distributed combination must be GPL-compatible.
license = "GPL-3.0-or-later"
requires-python = ">=3.11"
authors = [{ name = "Jaret Arnold" }]
keywords = [
    "mcp",
    "model-context-protocol",
    "plant-breeding",
    "simulation",
    "alphasimr",
    "quantitative-genetics",
    "genomic-selection",
]
classifiers = [
    "Development Status :: 3 - Alpha",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]
dependencies = [
    # 2.x only. The old 1.28.1 floor was a SECURITY floor rather than a feature
    # one, and every 2.x release clears it. The range MOVES rather than widening
    # to <3: this package imports mcp.server.mcpserver, which does not exist in
    # 1.x, so a range spanning both majors could resolve to a version that cannot
    # import the server. mcp 2.x requires Python >=3.10, below our >=3.11 floor.
    "mcp>=2,<3",
    # rpy2 >=3.6 needs a newer R than 4.3. Upstream's own docs for 3.6.x state
    # **R >= 4.5** (rpy2.github.io/doc/latest/html/overview.html) -- this comment
    # previously said 4.4, which was wrong and understated the gap.
    #
    # The mechanism is real and observed, not inferred: dependabot proposed
    # `<3.6` -> `<3.7` (PR #25), and all three test jobs died in
    # `openrlib.rlib.R_getVar(...)` with "The embedded R is not initialized."
    # against R 4.3.
    #
    # Deliberately NOT claiming which R the distros ship: CRAN publishes 4.5
    # packages for current Ubuntu, so "Debian/Ubuntu ship 4.3" (also previously
    # asserted here) depends on whether you use the distro archive or CRAN's.
    # What is verified is that R 4.3.x is still widely in use and is what this
    # package is developed against.
    "rpy2>=3.5,<3.6",
    "numpy>=1.26",
    # pydantic raises PydanticUserError on stdlib TypedDict under Python < 3.12,
    # which breaks outputSchema generation on 3.11 only.
    "typing-extensions>=4.12",
]

[project.urls]
Homepage = "https://github.com/musharna/breedsim-mcp"
Repository = "https://github.com/musharna/breedsim-mcp"
Issues = "https://github.com/musharna/breedsim-mcp/issues"
Changelog = "https://github.com/musharna/breedsim-mcp/blob/master/CHANGELOG.md"

[project.scripts]
breedsim-mcp = "breedsim_mcp.server:main"

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

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

[tool.hatch.build.targets.sdist]
# hatchling's `packages` covers the WHEEL ONLY. Without an explicit allow-list
# the sdist packs .claude/ and docs/. Verify with `tar tzf`, not `git ls-files`.
include = [
    "src/**",
    "tests/**",
    "README.md",
    "CHANGELOG.md",
    "CONTRIBUTING.md",
    "SECURITY.md",
    "LICENSE",
    "CITATION.cff",
    "NOTICE",
    "pyproject.toml",
]
exclude = [".claude", "docs", "dist"]

[tool.uv]
# Do NOT build against a conda interpreter. conda ships its own libstdc++.so.6,
# which shadows the system one and is older than system libicuuc requires, so
# rpy2's dlopen of libR.so dies with "GLIBCXX_3.4.30 not found". A uv-managed
# CPython links against the system C++ runtime and works.
python-preference = "only-managed"

[tool.ruff]
# ruff formats Python code blocks embedded in Markdown; docs/ holds the design
# and plan, whose quoted snippets are a record and must not be rewritten.
extend-exclude = ["docs"]

[dependency-groups]
# jsonschema validates server.json against the registry's own published schema
# (vendored at tests/server.schema.json) so registry-side constraints fail here
# rather than in the publish workflow, which only runs once the tag is already
# cut -- which is exactly how v0.4.0 shipped before being refused with a 422.
dev = ["pytest>=8.0", "ruff>=0.6", "jsonschema>=4.0"]

[tool.mutmut]
source_paths = ["src"]