pyproject.toml

[project]
name = "deepcritical"
version = "0.1.0"
description = "AI-Native Drug Repurposing Research Agent"
readme = "README.md"
requires-python = ">=3.11"
dependencies = [
    "pydantic>=2.7",
    "pydantic-settings>=2.2",
    "pydantic-ai>=0.0.16",
    "openai>=1.0.0",
    "anthropic>=0.18.0",
    "httpx>=0.27",
    "beautifulsoup4>=4.12",
    "xmltodict>=0.13",
    "huggingface-hub>=0.20.0",
    "gradio[mcp,oauth]>=6.0.0",
    "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)
    "pydantic-graph>=1.22.0",
    "limits>=3.0", # Rate limiting
    "duckduckgo-search>=5.0", # Web search
    "llama-index-llms-huggingface>=0.6.1",
    "llama-index-llms-huggingface-api>=0.6.1",
    "llama-index-vector-stores-chroma>=0.5.3",
    "llama-index>=0.14.8",
    "tokenizers>=0.22.0,<=0.23.0",
    "transformers>=4.57.2",
    "chromadb>=0.4.0",
    "rpds-py>=0.29.0",  # Python implementation of rpds (required by chromadb on Windows)
    "sentence-transformers>=2.2.0",
    "numpy<2.0",
    "agent-framework-core>=1.0.0b251120,<2.0.0",
    "modal>=0.63.0",
    "llama-index-llms-openai>=0.6.9",
    "llama-index-embeddings-openai>=0.5.1",
    "pydantic-ai-slim[huggingface]>=0.0.18",
    "pytest>=9.0.1",
    "pytest-cov>=7.0.0",
]

[project.optional-dependencies]
dev = [
    "pytest>=9.0.1",
    "pytest-asyncio>=1.3.0",
    "pytest-sugar>=1.1.1",
    "pytest-cov>=7.0.0",
    "pytest-mock>=3.15.1",
    "respx>=0.22.0",
    "typer>=0.9.0",
    "ruff>=0.14.6",
    "mypy>=1.18.2",
    "pre-commit>=3.7",
    "mkdocs>=1.5.0",
    "mkdocs-material>=9.7.0",
    "mkdocs-mermaid2-plugin>=1.2.3",
    "mkdocs-minify-plugin>=0.8.0",
    "mkdocs-codeinclude-plugin>=0.2.1",
    "mkdocs-macros-plugin>=1.5.0",
    "pymdown-extensions>=10.17.2",
]

[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"]
exclude = [
    "tests/",
    "examples/",
    "reference_repos/",
    "folder/",
]

[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)
    "E501",     # Line too long (ignore line length violations)
    "RUF100",   # Unused noqa (version differences between local/CI)
]

[tool.ruff.lint.per-file-ignores]
"src/app.py" = ["PLR0915"]  # Too many statements (Gradio UI setup is complex)
".pre-commit-hooks/run_pytest_with_sync.py" = ["PLR0915"]  # Too many statements (pre-commit hook with comprehensive cache cleaning)

[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
explicit_package_bases = true
mypy_path = "."
exclude = [
    "^reference_repos/",
    "^examples/",
    "^folder/",
    "^src/app\\.py$",  # Gradio UI setup - ignore mypy checks
]

# ============== PYTEST CONFIG ==============
[tool.pytest.ini_options]
testpaths = ["tests"]
asyncio_mode = "auto"
addopts = [
    "-v",
    "--tb=short",
    "--strict-markers",
    "-p",
    "no:logfire",
]
# Suppress known warnings that don't indicate test failures
# These are from third-party libraries and don't affect test correctness
filterwarnings = [
    # Pydantic deprecation warnings from unittest.mock introspection
    # These occur when mock tries to introspect Pydantic models
    "ignore::pydantic.warnings.PydanticDeprecatedSince20",
    "ignore::pydantic.warnings.PydanticDeprecatedSince211",
    # Gradio UI warnings (not relevant for unit tests)
    "ignore::UserWarning:gradio.components.dropdown",
    "ignore::UserWarning:gradio.oauth",
    # Pattern-based filters for Pydantic deprecation messages (catch-all)
    "ignore:The `__fields__` attribute is deprecated.*",
    "ignore:The `__fields_set__` attribute is deprecated.*",
    "ignore:Accessing the 'model_computed_fields' attribute.*",
    "ignore:Accessing the 'model_fields' attribute.*",
    # Also catch warnings from unittest.mock module
    "ignore::DeprecationWarning:unittest.mock",
]
# Note: pytest only runs test files, so source files don't need exclusion
markers = [
    "unit: Unit tests (mocked)",
    "integration: Integration tests (real APIs)",
    "slow: Slow tests",
    "openai: Tests that require OpenAI API key",
    "huggingface: Tests that require HuggingFace API key or use HuggingFace models",
    "embedding_provider: Tests that require API-based embedding providers (OpenAI, etc.)",
    "local_embeddings: Tests that use local embeddings (sentence-transformers, ChromaDB)",
]

# ============== COVERAGE CONFIG ==============
[tool.coverage.run]
source = ["src"]
omit = [
    "*/__init__.py",
    "src/app.py",  # Exclude Gradio UI from coverage
]

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