[tool.poetry]
name = "plantai-rag"
version = "0.1.0"
description = "Plant gene-family literature RAG and knowledge extraction system"
authors = ["PlantAI-rag maintainers"]
readme = "README.md"
packages = [{include = "src"}]
#package-mode = false


[tool.poetry.dependencies]
python = "^3.11"
# Core
pydantic = "^2.5.0"
pydantic-settings = "^2.1.0"
python-dotenv = "^1.0.0"

# LLM
openai = "^1.12.0"
zhipuai = "^2.0.0"
httpx = "^0.26.0"

# Agent Framework
langgraph = "^0.2.0"
langchain = "^0.3.0"
langchain-core = "^0.3.0"
langchain-community = "^0.3.0"
langsmith = "^0.1.0"

# Vector Store
qdrant-client = "^1.7.0"
pymilvus = "^2.3.0"

# Database
sqlalchemy = "^2.0.0"
asyncpg = "^0.29.0"
redis = "^5.0.0"

# Web Framework
fastapi = "^0.109.0"
uvicorn = "^0.27.0"
python-multipart = "^0.0.6"
websockets = "^12.0"

# Bioinformatics
biopython = "^1.83"
pymupdf = "^1.24.0"
pandas = "^2.1.0"
openpyxl = "^3.1.0"
xlrd = "^2.0.1"
python-docx = "^1.1.0"
requests = "^2.31.0"

# Utilities
pyyaml = "^6.0.1"
rich = "^13.7.0"
loguru = "^0.7.2"
tenacity = "^8.2.3"
aiofiles = "^23.2.1"
neo4j = "^6.1.0"

[tool.poetry.group.dev.dependencies]
pytest = "^7.4.0"
pytest-asyncio = "^0.23.0"
pytest-cov = "^4.1.0"
ruff = "^0.1.0"
mypy = "^1.8.0"
chardet = "^7.0.1"
jieba = "^0.42.1"

[tool.poetry.scripts]
start = "api.main:run"

[build-system]
requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api"

[tool.ruff]
line-length = 100
target-version = "py311"

[tool.mypy]
python_version = "3.11"
strict = true

[tool.pytest.ini_options]
testpaths = ["tests"]
norecursedirs = [
    "archive",
    "tests/archive",
]
python_files = [
    "test_functional_surface_parity.py",
    "test_api_app.py",
    "test_llm_definition_generator_config.py",
    "test_llm_provider_guardrails.py",
    "test_migration_requirements_audit.py",
    "test_methodology_alignment_real_case.py",
    "test_methodology_duplicate_rules.py",
    "test_methodology_identification_inputs.py",
    "test_methodology_mineru_gpu_preflight.py",
    "test_methodology_plan_bridge.py",
    "test_methodology_qa_sandbox.py",
    "test_neo4j_config_env.py",
    "test_open_source_audit.py",
    "test_paper_metadata_enricher_identity.py",
    "test_project_path_fallbacks.py",
    "test_runtime_surface_manifest.py",
    "test_temporal.py",
    "test_vlm_image_extractor_config.py",
    "test_v16_batch_runner.py",
    "test_v16_local_baseline.py",
    "test_v16_validation_contract.py",
]