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 (PubMed)
    "beautifulsoup4>=4.12", # HTML parsing
    "xmltodict>=0.13", # PubMed XML -> dict
    "huggingface-hub>=0.20.0", # Hugging Face Inference API
    # UI
    "gradio[mcp]>=6.0.0", # Chat interface with MCP server support (6.0 required for css in launch())
    # Utils
    "python-dotenv>=1.0", # .env loading
    "tenacity>=8.2", # Retry logic
    "structlog>=24.1", # Structured logging
    "requests>=2.32.5", # ClinicalTrials.gov (httpx blocked by WAF)
    "limits>=3.0", # Rate limiting
    "duckduckgo-search>=5.0", # Web search
]

[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
    "typer>=0.9.0",                  # Gradio CLI dependency for smoke tests

    # Quality
    "ruff>=0.4.0",
    "mypy>=1.10",
    "pre-commit>=3.7",
]
magentic = [
    "agent-framework-core>=1.0.0b251120,<2.0.0",  # Microsoft Agent Framework (PyPI)
]
embeddings = [
    "chromadb>=0.4.0",
    "sentence-transformers>=2.2.0",
]
modal = [
    # Mario's Modal code execution + LlamaIndex RAG
    "modal>=0.63.0",
    "llama-index>=0.11.0",
    "llama-index-llms-openai",
    "llama-index-embeddings-openai",
    "llama-index-vector-stores-chroma",
    "chromadb>=0.4.0",
]

[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)
    "PLR0911",  # Too many return statements (complex agent logic)
    "PLR2004",  # Magic values (statistical constants like p-values)
    "PLW0603",  # Global statement (singleton pattern for Modal)
    "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
exclude = [
    "^reference_repos/",
    "^examples/",
]

# ============== 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 for magentic mode (multi-agent orchestration)
# Version pinned to 1.0.0b* to avoid breaking changes. CI skips tests via pytest.importorskip