pyproject.toml

[build-system]
requires = ["setuptools>=68.0"]
build-backend = "setuptools.build_meta"

[project]
name = "amrex-agent"
version = "2.0.0"
description = "AI agent for AMReX-based simulation setup"
requires-python = ">=3.11"
authors = [
    {name = "Jean M. Sexton", email = "jmsexton@lbl.gov"}
]
readme = "README.md"
keywords = ["simulation", "AMReX", "multiphysics", "HPC", "AI"]

[tool.amrex_agent]
dependency_file = "environment.yaml"

[tool.pytest.ini_options]
testpaths = ["tests"]
norecursedirs = [".git", ".worktrees", "tools", "src", "reports", "*.egg-info", "_archive*", "__pycache__"]
python_files = "test_*.py"
python_functions = "test_*"
python_classes = "Test*"
addopts = [
    "-v",
    "--cov=src",
    "--cov-report=term-missing",
    "--tb=short",
    "--strict-markers",
    "--durations=10",
]
markers = [
    "unit: Unit tests (fast, isolated, mocked)",
    "functional: Unit tests exercising real components with minimal mocks",
    "mocked: Unit tests primarily using mocks or fakes",
    "e2e: End-to-end demo-driven smoke tests",
    "demo: Demo flows exercised via pytest",
    "disable_validators: Set PELE_DISABLED_VALIDATORS for test runs",
    "integration: Integration tests requiring external resources",
    "timeout: Per-test timeout (pytest-timeout compatibility)",
    "integration_l1: Architect + Reviewer (State Logic)",
    "integration_l2: + InputWriter (Filesystem I/O)",
    "integration_l3: + Analysis/Visualization (Output Parsing)",
    "integration_l4: + Runner (Execution/Shim)",
    "integration_full: L5 full pipeline tests",
    "architect_solver_selection: Architect Service - Solver Selection",
    "architect_context_retrieval: Architect Service - Context Retrieval",
    "architect_baseline_selection: Architect Service - Baseline Selection",
    "architect_modification_planning: Architect Service - Modification Planning",
    "architect_orchestration: Architect Service - Orchestration Logic",
    "architect_llm_planning: Architect Service - LLM Planning",
    "input_writer_schema_scraper: Input Writer - Schema Scraper",
    "input_writer_config_model_factory: Input Writer - Config Model Hydration tests",
    "input_writer_rule_engine: Input Writer - Rule Engine tests",
    "input_writer_inputs_file_writer: Input Writer - Inputs File Writer tests",
    "input_writer_rule_engine_orchestrator: Input Writer - Rule Engine Orchestrator tests",
    "input_writer_schema_composition: Input Writer - Schema Composition & Dependency Discovery",
    "technical_debt: Marks legacy code needing refactor (tracked but not blocking)",
    "performance: marks tests as performance/latency tests (skipped if indices not built)",
    "architecture: Architectural compliance tests (enforce design patterns)",
    "quality: Data quality tests (validate metadata consistency)",
    "real_repos: Tests against ../PeleC, ../warpx (auto-skip if not found)",
    "requires_filesystem: Tests that create files/directories",
    "requires_solver: Tests require a specific solver code name (args: AMReX, PeleC, WarpX, etc.)",
    "requires_indices: Tests require FAISS indices (args: faiss, level0, level1, level2, or index subdir)",
    "slow: Slower integration tests (may be skipped in CI)",
    "ci_fast: Fast smoke tests intended for CI selection",
    "skip: Skipped tests (use sparingly)",
    "use_real_services: Run tests with real services (not mocked)",
    "use_mock_services: Run tests with mocked services (default, fast)",
    "requires_repos: Tests require solver repositories to be available",
    "requires_schema: Tests require schema files to be available",
    "indexing_simple: Use simple indexing strategy (development approach, proven e2e)",
    "indexing_hierarchical: Use hierarchical indexing strategy (L0/L1/L2, experimental)",
    "indexing_override_static: Use override_static indexing strategy (no embeddings, baseline override required)",
]
asyncio_mode = "auto"

[tool.coverage.run]
source = ["src"]
omit = [
    "*/tests/*",
    "*/__pycache__/*",
    "*/venv/*",
    "*/.venv/*",
    "*/demo/*",
    "*/demo_*.py",
    "*/database/*",
    "*/docs/*",
    "*/tools/*",
    "*/test_langgraph_streaming.py",
    "*/mcp_server.py",
]
branch = true
relative_files = true

[tool.coverage.report]
precision = 2
show_missing = true
skip_covered = true
exclude_lines = [
    "pragma: no cover",
    "def __repr__",
    "raise AssertionError",
    "raise NotImplementedError",
    "if __name__ == .__main__.:",
    "if TYPE_CHECKING:",
    "@abstractmethod",
]

[tool.mypy]
python_version = "3.11"
warn_return_any = true
warn_unused_configs = true
disallow_untyped_defs = false
disallow_any_generics = false
check_untyped_defs = true
no_implicit_optional = true
warn_redundant_casts = true
warn_unused_ignores = true
warn_no_return = true
strict_equality = true
follow_imports = "normal"
show_error_codes = true

[[tool.mypy.overrides]]
module = ["faiss.*", "langchain.*", "anthropic.*", "utils.pele_tools.*", "amrex_tools.*"]
ignore_missing_imports = true

[tool.black]
line-length = 100
target-version = ['py311']
include = '\.pyi?$'
exclude = '''
/(
    \.git
  | \.venv
  | venv
  | build
  | dist
  | __pycache__
)/
'''

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

[tool.ruff.lint]
select = ["E", "W", "F", "I", "N", "UP", "B", "C4", "SIM", "D"]
ignore = ["E501", "B008", "C901", "D100", "D104", "D105"]

[tool.ruff.lint.pydocstyle]
convention = "numpy"

[tool.ruff.lint.per-file-ignores]
"tests/**/*.py" = ["F401", "F811"]

[tool.ruff.lint.isort]
known-first-party = ["src", "amrex_tools", "utils"]