pyproject.toml

[build-system]
requires = ["setuptools>=61", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "labtrust-gym"
version = "0.2.0"
description = "Multi-agent environment for hospital lab automation (PettingZoo/Gym style) with trust skeleton; first instance: pathology lab (blood sciences lane)."
readme = "README.md"
license = { text = "Apache-2.0" }
requires-python = ">=3.11"
authors = [{ name = "LabTrust-Gym contributors" }]
maintainers = [{ name = "LabTrust-Gym contributors" }]
keywords = [
    "gym",
    "multi-agent",
    "hospital-lab",
    "trust",
    "policy",
    "simulation",
    "pettingzoo",
    "gymnasium",
]
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: Apache Software License",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Topic :: Scientific/Engineering",
    "Topic :: Scientific/Engineering :: Artificial Intelligence",
]
dependencies = [
    "pyyaml>=6.0",
    "pydantic>=2.0",
    "jsonschema>=4.0",
    "networkx>=3.0",
    "numpy>=1.24",
    "cryptography>=46.0.5",
    "python-dotenv>=1.0",
]

[project.urls]
Homepage = "https://github.com/fraware/LabTrust-Gym"
Documentation = "https://fraware.github.io/LabTrust-Gym/"
Repository = "https://github.com/fraware/LabTrust-Gym"
"Bug Tracker" = "https://github.com/fraware/LabTrust-Gym/issues"

[project.optional-dependencies]
dev = [
    "pytest>=7.0",
    "pytest-timeout>=2.0",
    "pytest-cov>=4.0",
    "ruff>=0.1",
    "mypy>=1.0",
    "types-PyYAML>=6.0",
    "types-jsonschema>=4.0",
    "hypothesis>=6.0",
]
# PettingZoo Parallel API wrapper; install with: pip install -e ".[env]"
env = ["pettingzoo>=1.24", "gymnasium>=0.29"]
# .env loading is now a default dependency; [dotenv] kept for backward compatibility (no extra deps).
dotenv = []
# Enhanced CLI output (Rich formatting, progress); install with: pip install -e ".[cli]"
cli = ["rich>=13.0.0"]
# Plotting pipeline for study outputs; install with: pip install -e ".[plots]"
plots = ["matplotlib>=3.7", "pillow>=12.1.1"]
# Full dev/reuse: env + marl + docs + plots to minimize test skips; install with: pip install -e ".[full]"
full = [
    "pettingzoo>=1.24",
    "gymnasium>=0.29",
    "matplotlib>=3.7",
    "pillow>=12.1.1",
    "stable-baselines3>=2.0",
    "mkdocs>=1.5",
    "mkdocstrings[python]>=0.24",
]
# PPO/MARL baselines; install with: pip install -e ".[marl]"
marl = ["stable-baselines3>=2.0", "gymnasium>=0.29"]
# HPO for PPO (run_ppo_optuna); install with: pip install -e ".[marl,marl_hpo]"
marl_hpo = ["optuna>=3.0"]
# Documentation site; install with: pip install -e ".[docs]"
docs = ["mkdocs>=1.5", "mkdocstrings[python]>=0.24"]
# Live OpenAI backend (Structured Outputs); install with: pip install -e ".[llm_openai]"
# Base install remains unchanged; no network calls without this extra.
llm_openai = ["openai>=1.40", "urllib3>=2.6.3"]
# Live Anthropic backend; install with: pip install -e ".[llm_anthropic]"
llm_anthropic = ["anthropic>=0.39", "urllib3>=2.6.3"]
# Prime Intellect Inference (OpenAI-compatible client to api.pinference.ai); pip install -e ".[llm_prime_intellect]"
llm_prime_intellect = ["openai>=1.40", "urllib3>=2.6.3"]
# Online serve mode (rate limiting, auth, etc.); stdlib-only by default; add deps here if needed
online = []
# OpenTelemetry OTLP export for LLM traces; install with: pip install -e ".[otel]"
otel = ["opentelemetry-api>=1.20", "opentelemetry-sdk>=1.20", "opentelemetry-exporter-otlp-proto-http>=1.20"]
# MAPF/TAPF solvers (CBS, ECBS, LNS, RHCR); WHCA remains default when not installed
mapf = []
# OR solvers (CP-SAT for ORScheduler when use_cp_sat in policy); optional
or_solver = ["ortools>=9.0"]

# Extension points: other packages may add entries to these groups.
# See docs/extension_development.md for contracts.
[project.entry-points."labtrust_gym.domains"]
[project.entry-points."labtrust_gym.coordination_methods"]
[project.entry-points."labtrust_gym.tasks"]
[project.entry-points."labtrust_gym.invariant_handlers"]
[project.entry-points."labtrust_gym.security_suite_providers"]
[project.entry-points."labtrust_gym.safety_case_providers"]
[project.entry-points."labtrust_gym.metrics_aggregators"]
[project.entry-points."labtrust_gym.benchmark_pack_loaders"]

[project.scripts]
labtrust = "labtrust_gym.cli.main:main"

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

# Policy files (emits, schemas, zones, etc.). For release wheels, copy repo policy/ into src/labtrust_gym/policy before building.
[tool.setuptools.package-data]
labtrust_gym = ["policy/**"]

[tool.ruff]
target-version = "py311"
line-length = 120

[tool.ruff.lint]
select = ["E", "F", "I", "N", "W", "UP"]
ignore = [
    "E501",  # Line length 120: new code only; backlog incremental. See docs/reference/documentation_standards.md.
    "E402",  # Module level import not at top: intentional for lazy/conditional imports and sys.path setup.
    "N802",  # invalid-function-name: do_GET/do_POST etc. (stdlib BaseHTTPRequestHandler) only. See docs/reference/code_style_and_lint.md.
    "N806",  # non-lowercase-variable-in-function: constant-like names in function scope only. See docs/reference/code_style_and_lint.md.
    "N818",  # Exception name without Error suffix: existing exception names kept for API stability.
]

[tool.ruff.lint.per-file-ignores]
# Tests: allow unused variables (assertions/placeholders) and ambiguous names (e.g. loop var l).
"tests/**" = ["F841", "E741", "E731"]

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

[tool.mypy]
python_version = "3.11"
strict = true
warn_return_any = true
warn_unused_ignores = true
# Allow incremental cleanup: disable noisy codes that are widely present; re-enable as fixes land.
disable_error_code = [
    "no-any-return",
    "var-annotated",
    "type-arg",
    "attr-defined",
    "assignment",
    "arg-type",
    "operator",
    "index",
    "return-value",
    "union-attr",
    "call-overload",
    "list-item",
    "type-var",
    "unused-ignore",
    "no-untyped-call",
    "no-redef",
    "misc",
    "no-untyped-def",
    "call-arg",
    "comparison-overlap",
    "truthy-function",
]

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

[[tool.mypy.overrides]]
module = [
    "opentelemetry.*",
    "opentelemetry",
    "z3",
    "scipy.*",
    "scipy",
    "ortools.*",
    "anthropic",
    "networkx.*",
    "networkx",
    "tqdm",
    "optuna.*",
    "optuna",
]
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = [
    "rich",
    "rich.*",
    "openai",
    "dotenv",
    "python-dotenv",
]
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = [
    "matplotlib",
    "matplotlib.*",
    "gymnasium",
    "gymnasium.*",
    "stable_baselines3",
    "stable_baselines3.*",
]
ignore_missing_imports = true

[tool.coverage.run]
source = ["src/labtrust_gym"]
branch = false
omit = ["*/tests/*", "*/test_*"]

[tool.coverage.report]
exclude_lines = ["pragma: no cover", "def __repr__", "raise NotImplementedError"]
# Coverage ratchet: PR-blocking. See docs/ci.md for cadence and target.
fail_under = 54

[tool.pytest.ini_options]
testpaths = ["tests"]
pythonpath = ["src", "."]
addopts = "-q --timeout=120"
markers = [
    "metamorphic: metamorphic property tests (deterministic relations).",
    "determinism: failure physics / determinism tests (seeded).",
    "live: integration tests that call live APIs (require OPENAI_API_KEY, LABTRUST_RUN_LLM_LIVE=1).",
    "security: security fuzz and property tests (injection points, no action outside allowed).",
    "security_fuzz_stress: hypothesis-based security fuzz with higher max_examples (nightly); use --hypothesis-max-examples=500.",
    "slow: long-running tests (golden suite, package-release, heavy CLI); exclude with -m 'not slow'.",
]