pyproject.toml

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

[project]
name = "empathy-framework"
version = "5.3.0"
description = "AI collaboration framework with real LLM agent execution, AskUserQuestion tool integration, Socratic agent generation, progressive tier escalation (70-85% cost savings), meta-orchestration, dynamic agent composition (10 patterns including Anthropic-inspired), intelligent caching (85% hit rate), semantic workflow discovery, visual workflow editor, MCP integration for Claude Code, and multi-agent orchestration."
readme = {file = "README.md", content-type = "text/markdown"}
requires-python = ">=3.10"
license = {file = "LICENSE"}
authors = [
    {name = "Patrick Roebuck", email = "admin@smartaimemory.com"}
]
maintainers = [
    {name = "Smart-AI-Memory", email = "admin@smartaimemory.com"}
]
keywords = [
    "ai",
    "collaboration",
    "empathy",
    "anticipatory-ai",
    "systems-thinking",
    "llm",
    "claude",
    "memdocs",
    "level-5-ai",
    "code-inspection",
    "static-analysis",
    "code-quality",
    "sarif",
    "github-actions",
    "developer-tools"
]
classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Intended Audience :: Developers",
    "License :: OSI Approved :: Apache Software License",
    "Topic :: Software Development :: Libraries :: Application Frameworks",
    "Topic :: Scientific/Engineering :: Artificial Intelligence",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Operating System :: OS Independent",
]

# Core dependencies - minimal required for framework to function
dependencies = [
    "pydantic>=2.0.0,<3.0.0",
    "typing-extensions>=4.0.0,<5.0.0",
    "python-dotenv>=1.0.0,<2.0.0",
    "structlog>=23.0.0,<26.0.0",
    "defusedxml>=0.7.0,<1.0.0",
    "rich>=13.0.0,<14.0.0",  # Beautiful CLI output
    "typer>=0.9.0,<1.0.0",  # Better CLI commands
    "pyyaml>=6.0,<7.0",  # Required by workflows (bug_predict, etc.)
    "anthropic>=0.25.0,<1.0.0",  # Core LLM provider (direct SDK usage)
]
# NOTE: CrewAI and LangChain moved to optional dependencies in v4.4.0
# The "Crew" workflows use EmpathyLLMExecutor (Anthropic SDK) directly,
# not the actual CrewAI library. Install with: pip install empathy-framework[crewai]

[project.optional-dependencies]
# LLM providers (user chooses which they need)
anthropic = ["anthropic>=0.25.0,<1.0.0"]
openai = ["openai>=1.12.0,<2.0.0"]
# Note: google-generativeai is deprecated but still works; google-genai requires
# tenacity>=9.1.2 (now compatible with langchain>=0.3.0). Ready to migrate.
google = ["google-generativeai>=0.3.0,<1.0.0"]
llm = [
    "anthropic>=0.25.0,<1.0.0",
    "openai>=1.12.0,<2.0.0",
    "google-generativeai>=0.3.0,<1.0.0",
]

# MemDocs integration for long-term memory
memdocs = [
    "memdocs>=1.0.0",  # Published on PyPI
]

# LangChain ecosystem for agents/workflows
agents = [
    "langchain>=1.0.0,<2.0.0",
    "langchain-core>=1.2.5,<2.0.0",  # 1.2.5+ has security fixes
    "langchain-text-splitters>=0.3.9,<0.4.0",
    "langgraph>=1.0.0,<2.0.0",  # 1.0+ required for langgraph-checkpoint 3.0 (RCE fix)
    "langgraph-checkpoint>=3.0.0,<4.0.0",  # Security: GHSA-wwqv-p2pp-99h5 (RCE fix)
    "marshmallow>=4.1.2,<5.0.0",  # Security: GHSA-428g-f7cq-pgp5
]

# CrewAI for role-based multi-agent systems (DEPRECATED in v4.4.0)
# The meta-workflow system provides equivalent functionality using Anthropic SDK directly.
# See docs/CREWAI_MIGRATION.md for migration guide.
crewai = [
    "crewai>=0.1.0,<1.0.0",
    "langchain>=0.1.0,<2.0.0",
    "langchain-core>=1.2.6,<2.0.0",
]

# Hybrid caching for 70% cost reduction (v3.8.0+)
# Includes semantic similarity matching with sentence-transformers
cache = [
    "sentence-transformers>=2.0.0,<4.0.0",
    "torch>=2.0.0,<3.0.0",
    "numpy>=1.24.0,<3.0.0",
]

# Healthcare organizations - enterprise + compliance + healthcare plugins
# NOTE: Only install this if you need HIPAA/GDPR compliance features
healthcare = [
    # Everything in enterprise
    "anthropic>=0.25.0,<1.0.0",
    "openai>=1.12.0,<2.0.0",
    "google-generativeai>=0.3.0,<1.0.0",
    "memdocs>=1.0.0",
    "langchain>=1.0.0,<2.0.0",
    "langchain-core>=1.2.5,<2.0.0",
    "langchain-text-splitters>=0.3.9,<0.4.0",
    "langgraph>=1.0.0,<2.0.0",
    "langgraph-checkpoint>=3.0.0,<4.0.0",
    "marshmallow>=4.1.2,<5.0.0",
    "python-docx>=0.8.11,<1.0.0",
    "pyyaml>=6.0,<7.0",
    "fastapi>=0.109.1,<1.0.0",
    "uvicorn>=0.20.0,<1.0.0",
    "starlette>=0.40.0,<1.0.0",
    "bcrypt>=4.0.0,<5.0.0",
    "PyJWT[crypto]>=2.8.0",
    # OpenTelemetry for enterprise telemetry
    "opentelemetry-api>=1.20.0,<2.0.0",
    "opentelemetry-sdk>=1.20.0,<2.0.0",
    "opentelemetry-exporter-otlp-proto-grpc>=1.20.0,<2.0.0",
    # Healthcare-specific dependencies
    "redis>=5.0.0,<6.0.0",  # For session management and real-time alerts
]

software = [
    "python-docx>=0.8.11,<1.0.0",
    "pyyaml>=6.0,<7.0",
]

# Backend API server (optional)
backend = [
    "fastapi>=0.109.1,<1.0.0",  # CVE fix: PYSEC-2024-38
    "uvicorn>=0.20.0,<1.0.0",
    "starlette>=0.40.0,<1.0.0",  # CVE fix: GHSA-f96h, GHSA-2c2j
    "bcrypt>=4.0.0,<5.0.0",  # Password hashing (cost factor 12)
    "PyJWT[crypto]>=2.8.0",  # JWT auth - uses cryptography (no ecdsa CVE)
]

# LSP server for editor integration (optional)
lsp = [
    "pygls>=1.0.0,<2.0.0",
    "lsprotocol>=2023.0.0,<2024.0.0",
]

# Windows compatibility
windows = [
    "colorama>=0.4.6,<1.0.0",  # ANSI color support for Windows CMD
]

# OpenTelemetry backend for enterprise telemetry export
otel = [
    "opentelemetry-api>=1.20.0,<2.0.0",
    "opentelemetry-sdk>=1.20.0,<2.0.0",
    "opentelemetry-exporter-otlp-proto-grpc>=1.20.0,<2.0.0",
]

# Documentation dependencies
docs = [
    "mkdocs>=1.5.0,<2.0.0",
    "mkdocs-material>=9.4.0,<10.0.0",
    "mkdocstrings[python]>=0.24.0,<1.0.0",
    "mkdocs-with-pdf>=0.9.3,<1.0.0",  # PDF/ePub generation
    "pymdown-extensions>=10.0,<11.0",
]

# Development dependencies
dev = [
    "pytest>=7.0,<10.0",  # Updated upper bound for pytest 9.x
    "pytest-asyncio>=0.21,<2.0",  # Updated for pytest-asyncio 1.x
    "pytest-cov>=4.0,<8.0",  # Updated upper bound
    "pytest-mock>=3.14.0,<4.0",  # Mock fixtures for testing
    "pytest-xdist>=3.5.0,<4.0",  # Parallel test execution (4-8x faster)
    "pytest-testmon>=2.1.0,<3.0",  # Run only tests affected by changes
    "pytest-picked>=0.5.0,<1.0",  # Run tests for uncommitted changes
    "black>=24.3.0,<27.0",  # CVE fix: PYSEC-2024-48
    "mypy>=1.0,<2.0",
    "ruff>=0.1,<1.0",
    "coverage>=7.0,<8.0",
    "bandit>=1.7,<2.0",
    "pre-commit>=3.0,<5.0",  # Updated for pre-commit 4.x
    # Test dependencies for API and integration tests
    "httpx>=0.27.0,<1.0.0",  # For API testing
    "fastapi>=0.109.1,<1.0.0",  # For wizard API tests
    "requests>=2.28.0,<3.0.0",  # For notification tests
]

# Individual developers - lightweight, software development focused
developer = [
    # LLM providers
    "anthropic>=0.25.0,<1.0.0",
    "openai>=1.12.0,<2.0.0",
    "google-generativeai>=0.3.0,<1.0.0",
    # MemDocs integration
    "memdocs>=1.0.0",
    # Agents (updated for security fixes)
    "langchain>=1.0.0,<2.0.0",
    "langchain-core>=1.2.5,<2.0.0",  # 1.2.5+ has security fixes
    "langchain-text-splitters>=0.3.9,<0.4.0",
    "langgraph>=1.0.0,<2.0.0",  # 1.0+ required for langgraph-checkpoint 3.0 (RCE fix)
    "langgraph-checkpoint>=3.0.0,<4.0.0",  # Security: GHSA-wwqv-p2pp-99h5 (RCE fix)
    "marshmallow>=4.1.2,<5.0.0",  # Security: GHSA-428g-f7cq-pgp5
    # Software development plugins
    "python-docx>=0.8.11,<1.0.0",
    "pyyaml>=6.0,<7.0",
]

# Teams/enterprises - backend + authentication + compliance (excludes healthcare)
enterprise = [
    # Everything in developer
    "anthropic>=0.25.0,<1.0.0",
    "openai>=1.12.0,<2.0.0",
    "google-generativeai>=0.3.0,<1.0.0",
    "memdocs>=1.0.0",
    "langchain>=1.0.0,<2.0.0",
    "langchain-core>=1.2.5,<2.0.0",
    "langchain-text-splitters>=0.3.9,<0.4.0",
    "langgraph>=1.0.0,<2.0.0",
    "langgraph-checkpoint>=3.0.0,<4.0.0",
    "marshmallow>=4.1.2,<5.0.0",
    "python-docx>=0.8.11,<1.0.0",
    "pyyaml>=6.0,<7.0",
    # Backend API server with authentication
    "fastapi>=0.109.1,<1.0.0",
    "uvicorn>=0.20.0,<1.0.0",
    "starlette>=0.40.0,<1.0.0",
    "bcrypt>=4.0.0,<5.0.0",  # Secure password hashing
    "PyJWT[crypto]>=2.8.0",  # JWT authentication
    # OpenTelemetry for enterprise telemetry
    "opentelemetry-api>=1.20.0,<2.0.0",
    "opentelemetry-sdk>=1.20.0,<2.0.0",
    "opentelemetry-exporter-otlp-proto-grpc>=1.20.0,<2.0.0",
]

# Alias for backwards compatibility (maps to developer)
full = [
    # LLM providers
    "anthropic>=0.25.0,<1.0.0",
    "openai>=1.12.0,<2.0.0",
    "google-generativeai>=0.3.0,<1.0.0",
    # MemDocs integration
    "memdocs>=1.0.0",
    # Agents (updated for security fixes)
    "langchain>=1.0.0,<2.0.0",
    "langchain-core>=1.2.5,<2.0.0",  # 1.2.5+ has security fixes
    "langchain-text-splitters>=0.3.9,<0.4.0",
    "langgraph>=1.0.0,<2.0.0",  # 1.0+ required for langgraph-checkpoint 3.0 (RCE fix)
    "langgraph-checkpoint>=3.0.0,<4.0.0",  # Security: GHSA-wwqv-p2pp-99h5 (RCE fix)
    "marshmallow>=4.1.2,<5.0.0",  # Security: GHSA-428g-f7cq-pgp5
    # Plugins
    "python-docx>=0.8.11,<1.0.0",
    "pyyaml>=6.0,<7.0",
]

# Everything including development tools
all = [
    # LLM providers
    "anthropic>=0.25.0,<1.0.0",
    "openai>=1.12.0,<2.0.0",
    "google-generativeai>=0.3.0,<1.0.0",
    # MemDocs integration
    "memdocs>=1.0.0",
    # Agents (updated for security fixes)
    "langchain>=1.0.0,<2.0.0",
    "langchain-core>=1.2.5,<2.0.0",  # 1.2.5+ has security fixes
    "langchain-text-splitters>=0.3.9,<0.4.0",
    "langgraph>=1.0.0,<2.0.0",  # 1.0+ required for langgraph-checkpoint 3.0 (RCE fix)
    "langgraph-checkpoint>=3.0.0,<4.0.0",  # Security: GHSA-wwqv-p2pp-99h5 (RCE fix)
    "marshmallow>=4.1.2,<5.0.0",  # Security: GHSA-428g-f7cq-pgp5
    # Plugins
    "python-docx>=0.8.11,<1.0.0",
    "pyyaml>=6.0,<7.0",
    # Backend with authentication
    "fastapi>=0.109.1,<1.0.0",  # CVE fix
    "uvicorn>=0.20.0,<1.0.0",
    "starlette>=0.40.0,<1.0.0",  # CVE fix
    "bcrypt>=4.0.0,<5.0.0",  # Secure password hashing
    "PyJWT[crypto]>=2.8.0",  # JWT authentication
    # LSP
    "pygls>=1.0.0,<2.0.0",
    "lsprotocol>=2023.0.0,<2024.0.0",
    # Windows
    "colorama>=0.4.6,<1.0.0",
    # OpenTelemetry
    "opentelemetry-api>=1.20.0,<2.0.0",
    "opentelemetry-sdk>=1.20.0,<2.0.0",
    "opentelemetry-exporter-otlp-proto-grpc>=1.20.0,<2.0.0",
    # Documentation
    "mkdocs>=1.5.0,<2.0.0",
    "mkdocs-material>=9.4.0,<10.0.0",
    "mkdocstrings[python]>=0.24.0,<1.0.0",
    "mkdocs-with-pdf>=0.9.3,<1.0.0",
    "pymdown-extensions>=10.0,<11.0",
    # Dev tools
    "pytest>=7.0,<10.0",
    "pytest-asyncio>=0.21,<2.0",
    "pytest-cov>=4.0,<8.0",
    "black>=24.3.0,<27.0",  # CVE fix
    "mypy>=1.0,<2.0",
    "ruff>=0.1,<1.0",
    "coverage>=7.0,<8.0",
    "bandit>=1.7,<2.0",
    "pre-commit>=3.0,<5.0",
    "httpx>=0.27.0,<1.0.0",  # For API testing
    # Security constraint overrides for transitive dependencies
    "urllib3>=2.3.0,<3.0.0",  # CVE fix: GHSA-gm62, GHSA-2xpw
    "aiohttp>=3.10.0,<4.0.0",  # CVE fix: multiple CVEs
    "filelock>=3.16.0,<4.0.0",  # CVE fix: GHSA-w853
]

[project.scripts]
# Primary minimal CLI (v4.7.1+) - streamlined for automation/CI
empathy = "empathy_os.cli_minimal:main"

# Legacy entry points (for backwards compatibility)
empathy-legacy = "empathy_os.cli:main"
empathy-unified = "empathy_os.cli_unified:main"  # Previous unified CLI
empathy-scan = "empathy_software_plugin.cli:scan_command"
empathy-memory = "empathy_os.memory.control_panel:main"
empathy-inspect = "empathy_software_plugin.cli.inspect:main"
empathy-sync-claude = "empathy_llm_toolkit.cli.sync_claude:main"

[project.urls]
Homepage = "https://www.smartaimemory.com"
Documentation = "https://www.smartaimemory.com/framework-docs/"
"Getting Started" = "https://www.smartaimemory.com/framework-docs/tutorials/quickstart/"
FAQ = "https://www.smartaimemory.com/framework-docs/reference/FAQ/"
Book = "https://www.smartaimemory.com/book"
Repository = "https://github.com/Smart-AI-Memory/empathy-framework"
Issues = "https://github.com/Smart-AI-Memory/empathy-framework/issues"
Discussions = "https://github.com/Smart-AI-Memory/empathy-framework/discussions"
Changelog = "https://github.com/Smart-AI-Memory/empathy-framework/blob/main/CHANGELOG.md"

# Workflow plugin entry points for auto-discovery
[project.entry-points."empathy.workflows"]
code-review = "empathy_os.workflows.code_review:CodeReviewWorkflow"
doc-gen = "empathy_os.workflows.document_gen:DocumentGenerationWorkflow"
bug-predict = "empathy_os.workflows.bug_predict:BugPredictionWorkflow"
security-audit = "empathy_os.workflows.security_audit:SecurityAuditWorkflow"
perf-audit = "empathy_os.workflows.perf_audit:PerformanceAuditWorkflow"
test-gen = "empathy_os.workflows.test_gen:TestGenerationWorkflow"
refactor-plan = "empathy_os.workflows.refactor_plan:RefactorPlanWorkflow"
dependency-check = "empathy_os.workflows.dependency_check:DependencyCheckWorkflow"
# v4.0.0 CrewAI-based multi-agent workflows (production)
release-prep = "empathy_os.workflows.release_prep_crew:ReleasePreparationCrew"
health-check = "empathy_os.workflows.health_check_crew:HealthCheckCrew"
test-coverage-boost = "empathy_os.workflows.test_coverage_boost_crew:TestCoverageBoostCrew"
# Legacy single-agent versions
release-prep-legacy = "empathy_os.workflows.release_prep:ReleasePreparationWorkflow"
health-check-legacy = "empathy_os.workflows.health_check:HealthCheckWorkflow"
# Other workflows
secure-release = "empathy_os.workflows.secure_release:SecureReleasePipeline"
pro-review = "empathy_os.workflows.code_review_pipeline:CodeReviewPipeline"
pr-review = "empathy_os.workflows.pr_review:PRReviewWorkflow"

[tool.setuptools]
# Automatic package discovery
[tool.setuptools.packages.find]
where = ["src", "."]
namespaces = false
exclude = ["tests*", "*.tests*", "examples*", "docs*", "*.archive*", "build*", "dist*", "archived_wizards*", "wizards_consolidated*", "*.mypy_cache*", "*.__pycache__*"]

[tool.setuptools.package-dir]
empathy_os = "src/empathy_os"

[tool.setuptools.package-data]
"*" = ["*.yml", "*.yaml", "*.json", "*.txt", "*.md"]

# Black code formatter configuration
[tool.black]
line-length = 100
target-version = ['py310', 'py311', 'py312']
include = '\.pyi?$'
extend-exclude = '''
/(
  # directories
  \.eggs
  | \.git
  | \.hg
  | \.mypy_cache
  | \.tox
  | \.venv
  | build
  | dist
)/
'''

# Ruff linter configuration
[tool.ruff]
line-length = 100
target-version = "py310"
fix = true  # Auto-fix safe issues
exclude = [
    "tests/unit/wizards/",  # Generated wizard tests with syntax issues
    "website/",  # Next.js website - separate linting
    "docs/archive/",  # Archived code
    "examples/",  # Example code
    "dashboard/",  # Dashboard code
    "deployments/",  # Deployment scripts
    ".archive/",  # Archived files
    "src/empathy_os/workflows/new_sample_workflow1.py",  # Test workflow
    "src/empathy_os/workflows/test5.py",  # Test workflow
    "benchmarks/",  # Benchmark and test scripts
    "scaffolding/",  # Development scaffolding code
    "hot_reload/",  # Hot reload system
    "test_generator/",  # Test generator tools
    "workflow_patterns/",  # Experimental workflow patterns
    "workflow_scaffolding/",  # Workflow scaffolding tools
    "scripts/",  # Build and release scripts
    "services/",  # Service layer (external)
    "vscode-extension/",  # VSCode extension code
    "vscode-memory-panel/",  # VSCode memory panel
]

[tool.ruff.lint]
select = [
    "E",    # pycodestyle errors
    "W",    # pycodestyle warnings
    "F",    # pyflakes
    "I",    # isort
    "B",    # flake8-bugbear
    "C4",   # flake8-comprehensions
    "UP",   # pyupgrade
    "BLE",  # flake8-blind-except (catch bare except: clauses)
]
ignore = [
    "E501",  # line too long (handled by black)
    "B008",  # do not perform function calls in argument defaults
    "B904",  # raise exceptions with from err (too verbose for HTTPException pattern)
    "C901",  # too complex
]

[tool.ruff.lint.isort]
known-first-party = ["services", "empathy_llm_toolkit", "empathy_software_plugin", "empathy_os", "coach_wizards"]

[tool.ruff.lint.per-file-ignores]
"__init__.py" = ["F401"]  # unused imports in __init__.py
"test_*.py" = ["BLE001"]  # Test files can catch broad exceptions
"*_test.py" = ["BLE001"]  # Test files can catch broad exceptions
"tests/**/*.py" = ["BLE001", "B017"]  # Test files can catch/assert broad exceptions
"agents/**/*.py" = ["BLE001"]  # Agent files need broad exception handling for resilience
"backend/**/*.py" = ["BLE001", "E402"]  # Backend files need broad exception handling
"*_wizard.py" = ["BLE001"]  # Wizard files need broad exception handling
"*_agent.py" = ["BLE001"]  # Agent files need broad exception handling
"empathy_llm_toolkit/**/*.py" = ["BLE001"]  # Toolkit needs broad exception handling
"src/empathy_os/**/*.py" = ["BLE001"]  # Core framework needs broad exception handling
"*_adapter.py" = ["BLE001"]  # Adapter files need broad exception handling
"*_crew.py" = ["BLE001"]  # Crew files need broad exception handling
"dashboard/**/*.py" = ["BLE001"]  # Dashboard needs broad exception handling
"deployments/**/*.py" = ["BLE001"]  # Deployment scripts need broad exception handling
"docs/archive/**/*.py" = ["BLE001"]  # Archived code
"empathy_software_plugin/**/*.py" = ["BLE001"]  # Plugin needs broad exception handling
"examples/**/*.py" = ["BLE001"]  # Examples can use broad exception handling
"demo_*.py" = ["BLE001"]  # Demo files can use broad exception handling
"benchmark_*.py" = ["BLE001"]  # Benchmark scripts need broad exception handling for error reporting
"profile_*.py" = ["BLE001"]  # Profiling scripts need broad exception handling
"run_*.py" = ["BLE001"]  # Manual test runner scripts
"manual_*.py" = ["BLE001"]  # Manual test scripts
"benchmarks/**/*.py" = ["BLE001"]  # Benchmark directory - broad exception handling for test/benchmark scripts
"hot_reload/**/*.py" = ["BLE001"]  # Hot reload system needs broad exception handling
"scaffolding/**/*.py" = ["BLE001"]  # Scaffolding code - development tools
"test_generator/**/*.py" = ["BLE001"]  # Test generator - development tools
"workflow_patterns/**/*.py" = ["BLE001"]  # Workflow patterns - development/experimental
"workflow_scaffolding/**/*.py" = ["BLE001"]  # Workflow scaffolding - development tools
"scripts/**/*.py" = ["BLE001"]  # Build and release scripts need broad exception handling
"services/**/*.py" = ["BLE001"]  # Service layer needs broad exception handling
"vscode-extension/**/*.py" = ["BLE001"]  # VSCode extension scripts
"vscode-memory-panel/**/*.py" = ["BLE001"]  # VSCode memory panel scripts

# MyPy type checker configuration
[tool.mypy]
python_version = "3.10"
mypy_path = "src"
explicit_package_bases = true
exclude = [
    "10_9_2025_ai_nurse_florence/",
    "anthropic-cookbook/",
    "salvaged/",
    "site/",
    "ebook-site/",
    "website/",
    "agents/",  # Root-level agents dir (not part of main packages)
    "examples/",  # Example scripts (not part of main packages)
    "src/",  # Exclude src/ as top-level package (use via mypy_path instead)
    "build/",  # Build artifacts
    "backend/",  # Backend service (separate project)
    "scripts/",  # Utility scripts (not production code)
    "docs/",  # Documentation scripts
    "book-indesign/",  # Book publishing scripts
    "dashboard/",  # Dashboard (separate project)
    "archived_wizards/",  # Archived code
    "wizards_consolidated/",  # Consolidated wizards (separate)
    "coach_wizards/",  # Coach wizards (separate package)
    "tests/test_wizard_site_comprehensive.py",  # Large test file
    "tests/test_plugin_registry.py",  # Mock-heavy test file
]
warn_return_any = true
warn_unused_configs = true
disallow_untyped_defs = false
disallow_incomplete_defs = false
check_untyped_defs = false
disallow_untyped_decorators = false
no_implicit_optional = true
warn_redundant_casts = true
warn_unused_ignores = true
warn_no_return = true
follow_imports = "normal"
ignore_missing_imports = true

# Pytest configuration
[tool.pytest.ini_options]
minversion = "7.0"
testpaths = ["tests"]
python_files = ["test_*.py", "*_test.py"]
python_classes = ["Test*"]
python_functions = ["test_*"]
# Exclude pre-existing failing tests (tracked for v4.0.3)
# - wizards_consolidated module missing (2 test files)
# - test_generator mock issues (1 test file)
norecursedirs = [
    "tests/unit/test_generator",  # Mock issues with __file__ attribute
]
addopts = [
    "--verbose",
    "--cov=empathy_os",
    "--cov=empathy_llm_toolkit",
    "--cov=empathy_software_plugin",
    "--cov=empathy_healthcare_plugin",
    "--cov-report=html",
    "--cov-report=term-missing",
    "--cov-report=xml",
    "--cov-fail-under=55",
    "--asyncio-mode=auto",
    "--ignore=tests/test_base_wizard_exceptions.py",  # Missing wizards_consolidated module
    "--ignore=tests/test_wizard_api_integration.py",  # Missing wizards_consolidated module
]
markers = [
    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
    "integration: marks tests as integration tests",
    "unit: marks tests as unit tests",
    "security: marks tests as security-focused",
    "performance: marks tests as performance benchmarks",
    "llm: marks tests that require LLM API access",
    "network: marks tests that require network/internet access (skip in CI with '-m \"not network\"')",
]
filterwarnings = [
    "ignore::DeprecationWarning",
    "ignore::PendingDeprecationWarning",
]

# Coverage configuration
[tool.coverage.run]
source = ["empathy_os", "empathy_llm_toolkit", "empathy_software_plugin", "empathy_healthcare_plugin"]
omit = [
    "*/tests/*",
    "*/test_*.py",
    "*/__pycache__/*",
    "*/site-packages/*",
    # Deprecated/Example modules excluded from coverage (v4.4.0)
    "*/agent_factory/crews/*",  # CrewAI deprecated - use meta-workflows
    "*/agent_factory/adapters/autogen_adapter.py",  # Deprecated adapter
    "*/agent_factory/adapters/crewai_adapter.py",  # CrewAI deprecated
    "*/agent_factory/adapters/haystack_adapter.py",  # Deprecated adapter
    "*/agent_factory/adapters/langchain_adapter.py",  # Use native adapter
    "*/agent_factory/memory_integration.py",  # Optional integration module
    "*/agent_factory/resilient.py",  # Optional resilience module
    "*/*_example.py",  # Example files
    "*/cli/sync_claude.py",  # CLI tool, tested via integration
    # Utility modules with low criticality
    "*/utils/tokens.py",  # Token utilities
    "*/security/audit_logger.py",  # Optional audit logging
    "*/security/secure_memdocs.py",  # Optional secure memory
    # Pattern modules (optional pattern analysis)
    "*/pattern_confidence.py",
    "*/pattern_resolver.py",
    "*/pattern_summary.py",
    "*/git_pattern_extractor.py",
    "*/code_health.py",  # Optional code health analysis
    # Wizard examples (not core functionality)
    "*/wizards/patient_assessment_wizard.py",  # Healthcare-specific
    "*/wizards/healthcare_wizard.py",  # Healthcare-specific
    "*/wizards/technology_wizard.py",  # Example wizard
    "*/wizards/customer_support_wizard.py",  # Example wizard
]
branch = true

[tool.coverage.report]
precision = 2
show_missing = true
skip_covered = false
# Coverage threshold - increase as tests improve (target: 80%)
fail_under = 70
exclude_lines = [
    "pragma: no cover",
    "def __repr__",
    "raise AssertionError",
    "raise NotImplementedError",
    "if __name__ == .__main__.:",
    "if TYPE_CHECKING:",
    "class .*\\bProtocol\\):",
    "@(abc\\.)?abstractmethod",
]