med-paper-assistant/pyproject.toml at master · u9401066/med-paper-assistant · GitHub

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[project]
name = "med-paper-assistant"
version = "0.5.1"
description = "A medical paper writing assistant using MCP support"
readme = "README.md"
requires-python = ">=3.12"
license = "Apache-2.0"
authors = [{ name = "Eric", email = "medpaper@example.com" }]
keywords = ["medical", "paper", "assistant", "mcp", "pubmed"]

# ============================================
# 核心依賴 (最小化 - 純 MCP 架構)
# ============================================
dependencies = [
    "mcp>=1.0.0",
    "pydantic>=2.0.0",
    "pandas>=2.0.0",
    "tabulate>=0.9.0",
    "python-docx>=1.0.0",
    "requests>=2.28.0",
    "pyyaml>=6.0.0",
    "structlog>=25.5.0",
    "scipy>=1.17.0",
    "pypandoc>=1.16.2",
    "citeproc-py>=0.6.0",
]

# ============================================
# 可選依賴 (功能擴展)
# ============================================
[project.optional-dependencies]
# 開發模式：直接使用 submodule
pubmed = [
    "biopython>=1.80",
    "pubmed-search-mcp",
]
creativity = [
    "creativity-generation-unit",
]
analysis = [
    "matplotlib>=3.7.0",
    "scipy>=1.10.0",
    "seaborn>=0.12.0",
    "pypdf>=3.0.0",
]
# 學術出版工具鏈（CSL 引用 + Pandoc 匯出）
publishing = [
    "pypandoc>=1.13",
    "lxml>=4.9.0",
]
# 完整安裝（開發用）
all = [
    "med-paper-assistant[pubmed,creativity,analysis,publishing]",
]
dev = [
    "pytest>=7.0.0",
    "pytest-cov>=4.0.0",
    "pytest-asyncio>=0.21.0",
    "ruff>=0.1.0",
    "mypy>=1.0.0",
]

[project.scripts]
med-paper-assistant = "med_paper_assistant:run_server"

[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[tool.hatch.build.targets.wheel]
packages = ["src/med_paper_assistant"]

# ============================================
# 依賴群組 (uv 推薦格式)
# ============================================
[dependency-groups]
dev = [
    "pytest>=7.0.0",
    "pytest-cov>=4.0.0",
    "pytest-asyncio>=0.21.0",
    "ruff>=0.1.0",
    "mypy>=1.0.0",
    "bandit>=1.9.2",
    "vulture>=2.14",
    "pre-commit>=4.5.1",
    "pytest-timeout>=2.0.0",
    "types-requests>=2.28.0",
    "types-tabulate>=0.9.0",
    "types-pyyaml>=6.0.12.20250915",
]

# ============================================
# uv 工具配置：Submodule 可編輯安裝
# ============================================
[tool.uv.sources]
pubmed-search-mcp = { path = "integrations/pubmed-search-mcp", editable = true }
creativity-generation-unit = { path = "integrations/cgu", editable = true }

# ============================================
# Ruff 程式碼品質工具
# ============================================
[tool.ruff]
line-length = 100
target-version = "py312"
extend-exclude = ["vscode-extension/bundled"]

[tool.ruff.lint]
select = ["E", "F", "I", "W"]
ignore = ["E501"]

# ============================================
# Pytest 配置
# ============================================
[tool.pytest.ini_options]
testpaths = ["tests"]
python_files = ["test_*.py"]
asyncio_mode = "auto"
addopts = "-m 'not integration and not slow'"
timeout = 60
markers = [
    "slow: marks tests as slow (deselect with '-m not slow')",
    "integration: marks tests requiring external services",
]

# ============================================
# MyPy 類型檢查
# ============================================
[tool.mypy]
python_version = "3.12"
warn_return_any = true
warn_unused_configs = true
warn_unreachable = true
ignore_missing_imports = true
# Disable checks that conflict with python-docx / loosely-typed JSON APIs
disable_error_code = [
    "no-any-return",      # JSON/dict returns often Any
    "attr-defined",       # python-docx types not fully annotated
    "valid-type",         # python-docx Document type issues
]

[[tool.mypy.overrides]]
module = [
    "docx.*",
    "pandas.*",
    "scipy.*",
    "matplotlib.*",
]
ignore_errors = true

# ============================================
# Bandit 安全性掃描
# ============================================
[tool.bandit]
targets = ["src"]
skips = ["B101"]  # assert is fine in non-production code