pyproject.toml

[build-system]
requires = ["hatchling>=1.24"]
build-backend = "hatchling.build"

[project]
name = "uniprot-mcp-server"
version = "1.3.0"
description = "Model Context Protocol server for the UniProt protein knowledgebase. Install: pip install uniprot-mcp-server"
readme = "README.md"
requires-python = ">=3.11"
license = "Apache-2.0"
license-files = ["LICENSE", "NOTICE"]
keywords = [
    "mcp", "model-context-protocol", "mcp-server", "uniprot", "protein-database",
    "bioinformatics", "proteins", "swiss-prot", "biology", "llm-tools",
    "anthropic", "claude", "provenance", "reproducibility", "alphafold",
    "clinvar", "drug-discovery",
]
authors = [
    { name = "Santiago Maniches", email = "santiago.maniches@gmail.com" },
]
maintainers = [
    { name = "Santiago Maniches", email = "santiago.maniches@gmail.com" },
    { name = "TOPOLOGICA LLC", email = "santiago.maniches@gmail.com" },
]
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "Intended Audience :: Developers",
    "License :: OSI Approved :: Apache Software License",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Software Development :: Libraries :: Python Modules",
    "Typing :: Typed",
]
dependencies = [
    "httpx>=0.27",
    "mcp>=1.2",
]

[project.optional-dependencies]
test = [
    "pytest>=8.0",
    "pytest-asyncio>=0.23",
    "pytest-cov>=5.0",
    "pytest-socket>=0.7",
    "respx>=0.21",
    "hypothesis>=6.100",
    "syrupy>=4.6",
]
dev = [
    "ruff>=0.6",
    "mypy>=1.10",
    "bandit>=1.7",
    "pip-audit>=2.7",
    "pre-commit>=3.7",
    "interrogate>=1.7",
]
docs = [
    "mkdocs>=1.6",
    "mkdocs-material>=9.5",
]

[project.urls]
Homepage = "https://topologica.ai"
Repository = "https://github.com/smaniches/uniprot-mcp"
Documentation = "https://smaniches.github.io/uniprot-mcp/"
Issues = "https://github.com/smaniches/uniprot-mcp/issues"
Changelog = "https://github.com/smaniches/uniprot-mcp/blob/main/CHANGELOG.md"
"Author ORCID" = "https://orcid.org/0009-0005-6480-1987"
Organization = "https://topologica.ai"

[project.scripts]
uniprot-mcp = "uniprot_mcp.server:main"
# Alias matching the PyPI distribution name, so the MCP Registry launch
# command `uvx uniprot-mcp-server` resolves to a console script. Both
# entry points target the same callable; the bare `uniprot-mcp` is kept
# for back-compat.
uniprot-mcp-server = "uniprot_mcp.server:main"

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

[tool.hatch.build.targets.sdist]
include = [
    "src/uniprot_mcp/**",
    "README.md",
    "LICENSE",
    "NOTICE",
    "CHANGELOG.md",
    "CITATION.cff",
    "ARCHITECTURE.md",
    "tests/**",
]
exclude = [
    "**/__pycache__",
    "**/.pytest_cache",
    "**/.mypy_cache",
    "**/.ruff_cache",
]

[tool.pytest.ini_options]
minversion = "8.0"
asyncio_mode = "auto"
testpaths = ["tests"]
addopts = [
    "--strict-markers",
    "--strict-config",
    "-ra",
    "--disable-socket",
    "--allow-unix-socket",
    "--allow-hosts=127.0.0.1,::1",
]
markers = [
    "integration: live UniProt REST API; opt-in with --integration",
    "mcp_protocol: spawns the MCP server as a subprocess",
]
filterwarnings = [
    "error",
    "ignore::DeprecationWarning:pydantic.*",
    "ignore::DeprecationWarning:mcp.*",
]

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

[tool.coverage.report]
# Gate enforced at 100% line + branch across the package. The coverage
# uplift (chore/coverage-100) restored the v1.0.0 100% level after the
# v1.0.1 -> v1.1.x clinical/biomedical work had let it drift to ~92%.
# Two genuinely-unreachable arcs carry a justified ``# pragma: no cover``
# so they do not block the gate:
#   - client.py version-lookup ``except``: import-time fallback to "dev"
#     when running uninstalled; exercising it requires a module reload
#     that breaks exception-class identity across the package.
#   - server.py target-dossier FASTA-fetch ``except``: non-fatal
#     chemistry fallback.
# ``_extract_provenance`` reads the accept header directly from
# ``response.request``: the function also reads ``response.url`` (which
# httpx derives from the request), so the request is always present and
# the read needs no guard or pragma.
# Every other branch is covered by a genuine, assertion-bearing test.
# PRs that drop coverage below 100% should be rejected by review.
fail_under = 100
show_missing = true
skip_covered = false
exclude_lines = [
    "pragma: no cover",
    "raise NotImplementedError",
    "if __name__ == .__main__.:",
    "if TYPE_CHECKING:",
]

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

[tool.ruff.lint]
select = [
    "E", "W",   # pycodestyle
    "F",        # pyflakes
    "I",        # isort
    "B",        # bugbear
    "UP",       # pyupgrade
    "SIM",      # simplify
    "RUF",      # ruff-specific
    "N",        # pep8-naming
    "ASYNC",    # flake8-async
    "S",        # bandit-lite
    "PGH",      # pygrep-hooks: require an error code on every type:ignore / noqa
]
ignore = [
    "S101",     # use of assert in tests is fine
    "E501",     # line too long handled by formatter
]

[tool.ruff.lint.per-file-ignores]
"tests/**" = ["S", "N802", "N803"]

[tool.mypy]
python_version = "3.11"
strict = true
files = ["src/uniprot_mcp"]
mypy_path = "src"
disallow_untyped_decorators = false
warn_unused_ignores = true
show_error_codes = true

[[tool.mypy.overrides]]
module = ["mcp.*"]
ignore_missing_imports = true

[tool.bandit]
exclude_dirs = ["tests", "_scratch"]
skips = ["B101"]  # asserts in non-test code only, but we don't use them anyway

[tool.interrogate]
# Docstring-coverage gate over the package public + internal surface.
# Keys use underscores (interrogate accepts both; underscores are the
# documented form). `fail_under` is pinned at the exact current baseline
# (115/171 documented objects = 67.25%) and is a one-way ratchet: any
# regression fails CI; raising it is welcome.
# Run locally with: interrogate -c pyproject.toml src/uniprot_mcp
fail_under = 67.25
ignore_init_method = true
ignore_magic = true
ignore_nested_functions = true
ignore_module = false
ignore_private = false
ignore_semiprivate = false
exclude = ["tests", "_scratch"]