Spaces:
Running
Running
File size: 3,429 Bytes
069f0a0 4e2ccbf d7e5abb 069f0a0 1efef06 4e2ccbf 069f0a0 f5b2917 069f0a0 4e2ccbf 1efef06 069f0a0 1922dbd 3bacbf8 3aa91e9 069f0a0 15459e9 3aa91e9 15459e9 ecbc47b 069f0a0 15459e9 069f0a0 1922dbd 5a82171 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 |
[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
# UI
"gradio[mcp]>=5.0.0", # Chat interface
# 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)
]
[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",
]
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
# ============== 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
|