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[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
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