pyproject.toml

[project]
name = "deepcritical"
version = "0.1.0"
description = "AI-Native Drug Repurposing Research Agent"
readme = "README.md"
requires-python = ">=3.11"
dependencies = [
    # Core
    "pydantic>=2.7",
    "pydantic-settings>=2.2",      # For BaseSettings (config)
    "pydantic-ai>=0.0.16",          # Agent framework

    # AI Providers
    "openai>=1.0.0",
    "anthropic>=0.18.0",

    # HTTP & Parsing
    "httpx>=0.27",                   # Async HTTP client
    "beautifulsoup4>=4.12",          # HTML parsing
    "xmltodict>=0.13",               # PubMed XML -> dict

    # Search
    "duckduckgo-search>=6.0",        # Free web search

    # UI
    "gradio>=5.0",                   # Chat interface

    # Utils
    "python-dotenv>=1.0",            # .env loading
    "tenacity>=8.2",                 # Retry logic
    "structlog>=24.1",               # Structured logging
]

[project.optional-dependencies]
dev = [
    # Testing
    "pytest>=8.0",
    "pytest-asyncio>=0.23",
    "pytest-sugar>=1.0",
    "pytest-cov>=5.0",
    "pytest-mock>=3.12",
    "respx>=0.21",                   # Mock httpx requests

    # Quality
    "ruff>=0.4.0",
    "mypy>=1.10",
    "pre-commit>=3.7",
]
magentic = [
    "agent-framework-core",
]
embeddings = [
    "chromadb>=0.4.0",
    "sentence-transformers>=2.2.0",
]

[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[tool.hatch.build.targets.wheel]
packages = ["src"]

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

[tool.ruff.lint]
select = [
    "E",    # pycodestyle errors
    "F",    # pyflakes
    "B",    # flake8-bugbear
    "I",    # isort
    "N",    # pep8-naming
    "UP",   # pyupgrade
    "PL",   # pylint
    "RUF",  # ruff-specific
]
ignore = [
    "PLR0913",  # Too many arguments (agents need many params)
    "PLR0912",  # Too many branches (complex orchestrator logic)
    "PLC0415",  # Lazy imports for optional dependencies
    "E402",     # Module level import not at top (needed for pytest.importorskip)
    "RUF100",   # Unused noqa (version differences between local/CI)
]

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

# ============== MYPY CONFIG ==============
[tool.mypy]
python_version = "3.11"
strict = true
ignore_missing_imports = true
disallow_untyped_defs = true
warn_return_any = true
warn_unused_ignores = false

# ============== PYTEST CONFIG ==============
[tool.pytest.ini_options]
testpaths = ["tests"]
asyncio_mode = "auto"
addopts = [
    "-v",
    "--tb=short",
    "--strict-markers",
]
markers = [
    "unit: Unit tests (mocked)",
    "integration: Integration tests (real APIs)",
    "slow: Slow tests",
]

# ============== COVERAGE CONFIG ==============
[tool.coverage.run]
source = ["src"]
omit = ["*/__init__.py"]

[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",
    "if TYPE_CHECKING:",
    "raise NotImplementedError",
]

# Note: agent-framework-core is optional and installed locally for magentic mode
# CI skips tests that require it via pytest.importorskip