pyproject.toml

[project]
name = "communitymech"
version = "0.1.0"
description = "Microbial Community Mechanisms Knowledge Base - LinkML-based modeling with evidence validation"
authors = [
    {name = "CultureBotAI", email = "info@culturebot.ai"}
]
license = {text = "BSD-3-Clause"}
readme = "README.md"
requires-python = ">=3.10"

dependencies = [
    "linkml>=1.7.0",
    "linkml-runtime>=1.7.0",
    "linkml-term-validator>=0.1.0",
    "linkml-reference-validator>=0.1.0",
    "pydantic>=2.0.0",
    "pyyaml>=6.0",
    "click>=8.0.0",
    "jinja2>=3.0.0",
    "oaklib>=0.5.0",
    "requests>=2.31.0",
    "numpy>=1.24.0",
    "pandas>=2.0.0",
    "umap-learn>=0.5.0",
    "tqdm>=4.66.0",
]

[project.optional-dependencies]
dev = [
    "pytest>=7.0.0",
    "pytest-cov>=4.0.0",
    "black>=23.0.0",
    "ruff>=0.1.0",
    "mypy>=1.0.0",
    "pre-commit>=3.0.0",
]

koza = [
    "koza>=0.5.0",
    "biolink-model>=3.0.0",
]

validation = [
    "linkml-validator>=0.4.0",
]

llm = [
    "anthropic>=0.39.0",
    "rich>=13.0.0",
]

[project.scripts]
communitymech = "communitymech.cli:main"

[build-system]
requires = ["setuptools>=61.0", "wheel"]
build-backend = "setuptools.build_meta"

[tool.setuptools.packages.find]
where = ["src"]

[tool.black]
line-length = 100
target-version = ["py310", "py311", "py312"]

[tool.ruff]
line-length = 100
target-version = "py310"

[tool.ruff.lint]
select = ["E", "F", "I", "UP", "N", "S", "B", "A", "C4", "T20", "SIM"]
ignore = ["S101", "S603", "S607"]

[tool.pytest.ini_options]
testpaths = ["tests"]
python_files = ["test_*.py"]
python_classes = ["Test*"]
python_functions = ["test_*"]
markers = [
    "e2e: End-to-end tests that require API key (deselect with '-m \"not e2e\"')",
    "integration: Integration tests",
]
# By default, skip e2e tests (require explicit --e2e flag)
addopts = "-m 'not e2e'"

[tool.mypy]
python_version = "3.10"
warn_return_any = true
warn_unused_configs = true
disallow_untyped_defs = false