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",
    "deep-research-client[cyberian]>=0.2.4; python_version >= '3.12'",
    "types-PyYAML>=6.0.0",
    "types-requests>=2.31.0",
    "types-tqdm>=4.66.0",
    "pandas-stubs>=2.0.0",
]

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"
# The LinkML pythongen datamodel is fully regenerated by `just gen-python`
# and is not hand-edited, so style lints there create churn rather than
# signal. Exclude it from ruff (black still formats it via `just format`).
extend-exclude = ["src/communitymech/datamodel/communitymech.py"]

[tool.ruff.lint]
# T20 (print) is deliberately omitted: src/communitymech/ ships CLI
# entry points (cli.py, render_*, export/*, embedding/*, validators)
# that legitimately use print for user output, and tagging each call
# with `# noqa: T201` is louder than the rule is worth here.
select = ["E", "F", "I", "UP", "N", "S", "B", "A", "C4", "SIM"]
ignore = ["S101", "S603", "S607"]

[tool.ruff.lint.per-file-ignores]
# E501 (line-too-long) is suppressed in prompt-template modules because
# the strings are LLM prompt content; wrapping or splitting them would
# alter the rendered prompt.
"src/communitymech/llm/prompts.py" = ["E501"]

[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 is left off: most no-any-return reports here come from
# `requests.json()` / `.get()` chains feeding back into annotated return
# types. The annotations are correct; casting at every site is churn
# without improving safety. Re-enable if a real Any-leak hunt is needed.
warn_return_any = false
warn_unused_configs = true
disallow_untyped_defs = false
# The LinkML pythongen datamodel is fully regenerated by `just gen-python`
# and is not hand-edited, so type lints there create churn rather than
# signal. Excluded for the same reason ruff excludes it.
exclude = ["src/communitymech/datamodel/communitymech\\.py"]

# Optional/external modules without bundled type info — silence import-
# resolution noise. `anthropic` is an opt-in dep (LLM extra);
# `kg_microbe_browser` lives in a sibling repo. The internal modules
# under communitymech.datamodel are excluded above, but mypy still
# reports their import as an untyped follow-import.
[[tool.mypy.overrides]]
module = [
    "anthropic.*",
    "kg_microbe_browser.*",
    "communitymech.datamodel.*",
    "umap.*",
]
ignore_missing_imports = true