pyproject.toml

[build-system]
requires = ["hatchling", "hatch-vcs"]
build-backend = "hatchling.build"

[project]
name = "bertron-mcp"
dynamic = ["version"]
description = "An MCP for accessing the BERtron API"
requires-python = ">=3.12.19,<3.14"
license = "BSD-3-Clause"
keywords = ["mcp", "genome"]
dependencies = [
    "fastmcp>=2.7.1",
    "pytest>=8.4.1",
    "requests>=2.32.4",
    "urllib3>=2.0.0",
    "bertron-client @ git+https://github.com/ber-data/bertron-client.git@main"
]

[dependency-groups]
dev = [
    # Code quality and formatting
    "black>=23.0.0",
    "ruff>=0.1.0",
    "mypy>=1.0.0",
    # Testing
    "pytest>=8.0.0",
    "pytest-asyncio>=0.21.0",
    "pytest-cov>=4.0.0",
    # Build and packaging tools
    "hatch-vcs>=0.5.0",
    "hatchling>=1.27.0",
    "twine>=4.0.0",
    "hatch>=1.14.1",
    "types-requests>=2.32.4.20250611",
    "pip>=25.1.1",
]

[project.urls]
Homepage = "https://github.com/ber-data/bertron-mcp"
Repository = "https://github.com/ber-data/bertron-mcp"
Issues = "https://github.com/ber-data/bertron-mcp/issues"
Documentation = "https://github.com/ber-data/bertron-mcp#readme"

[project.scripts]
bertron-mcp = "bertron_mcp.__main__:main"

[tool.hatch.version]
source = "vcs"

[tool.hatch.metadata]
allow-direct-references = true

[tool.hatch.build.hooks.vcs]
version-file = "src/bertron_mcp/_version.py"

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

[tool.hatch.build.targets.sdist]
include = [
    "src",
    "tests",
    "README.md",
    "pyproject.toml",
]

# Ruff configuration
[tool.ruff]
line-length = 88
target-version = "py310"
exclude = ["src/bertron_mcp/_version.py"]

[tool.ruff.lint]
select = [
    "E",  # pycodestyle errors
    "W",  # pycodestyle warnings
    "F",  # pyflakes
    "I",  # isort
    "B",  # flake8-bugbear
    "C4", # flake8-comprehensions
    "UP", # pyupgrade
]
ignore = []

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

# Black configuration (if you prefer black over ruff format)
[tool.black]
line-length = 88
target-version = ['py310']

# MyPy configuration
[tool.mypy]
python_version = "3.10"
warn_unused_configs = true
show_error_codes = true
# Ignore missing stubs for third-party libraries
ignore_missing_imports = true
# Be less strict about Any returns from third-party libraries
warn_return_any = false
# Allow some untyped functions for now
disallow_untyped_defs = false
disallow_incomplete_defs = false

# Pytest configuration
[tool.pytest.ini_options]
minversion = "7.0"
addopts = "-ra -q --strict-markers"
testpaths = ["tests"]
python_files = ["test_*.py", "*_test.py"]
python_functions = ["test_*"]
markers = [
    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
    "integration: marks tests as integration tests",
]
filterwarnings = [
    "ignore::urllib3.exceptions.InsecureRequestWarning",
]

# Coverage configuration
[tool.coverage.run]
source = ["src/bertron_mcp"]
omit = ["src/bertron_mcp/_version.py"]

[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",
    "def __repr__",
    "if __name__ == .__main__.:",
    "raise AssertionError",
    "raise NotImplementedError",
]

# Deptry configuration
[tool.deptry]
# Map import names to package names
[tool.deptry.package_module_name_map]
pytest_asyncio = "pytest-asyncio"
pytest_cov = "pytest-cov"
hatch_vcs = "hatch-vcs"
types_requests = "types-requests"
fastmcp = "fastmcp"
pytest = "pytest"
bertron_client = "bertron-client"
black = "black"
ruff = "ruff"
mypy = "mypy"
hatchling = "hatchling"
twine = "twine"
hatch = "hatch"
pip = "pip"
urllib3 = "urllib3"

# Ignore specific error types for known false positives
[tool.deptry.per_rule_ignores]
DEP001 = ["bertron_mcp"]  # Missing deps: self-imports ok
DEP002 = [
    # Dev dependencies not used in main code
    "black", "ruff", "mypy", "pytest", "pytest-asyncio", "pytest-cov",
    "hatch-vcs", "hatchling", "twine", "hatch", "types-requests", "pip",
    # Indirect dependencies used by bertron-client
    "requests"
]