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

[project]
name = "preprint-fulltext"
version = "0.1.0"
description = "CLI + MCP toolkit that retrieves full text of bioRxiv/medRxiv/arXiv preprints as structured sections — grounding LLM/agent scientific reasoning and deep research — and builds embedding-ready corpora."
readme = "README.md"
requires-python = ">=3.11"
license = "BSD-3-Clause"
license-files = ["LICENSE"]
authors = [{ name = "Min Dai", email = "dai@broadinstitute.org" }]
keywords = ["biorxiv", "medrxiv", "preprint", "jats", "fulltext", "embeddings", "mcp", "openrxiv"]
classifiers = [
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
  "Intended Audience :: Science/Research",
  "Topic :: Scientific/Engineering :: Bio-Informatics",
  "Topic :: Text Processing :: Markup :: XML",
]
dependencies = [
  "pydantic>=2",
  "pydantic-settings>=2",
  "httpx>=0.27",
  "lxml>=5",
  "boto3>=1.34",
  "typer>=0.12",
  "rich>=13",
  "tiktoken>=0.7",
  "orjson>=3.9",
]

[project.optional-dependencies]
# The MCP server is built in (zero extra deps); no 'mcp' extra needed.
parquet = ["pyarrow>=15"]
embed = ["sentence-transformers>=2"]
openalex = ["pyalex>=0.15"]
test = [
  "pytest>=8",
  "respx>=0.21",
  "moto[s3]>=5",
  "pytest-recording>=0.13",
]
dev = [
  "preprint-fulltext[parquet,openalex,test]",
  "ruff>=0.5",
]

[project.urls]
Homepage = "https://github.com/genecell/preprint-fulltext"
Repository = "https://github.com/genecell/preprint-fulltext"

[project.scripts]
preprint-fulltext = "preprint_fulltext.cli:app"
preprint-fulltext-mcp = "preprint_fulltext.mcp_server:main"

[tool.hatch.build.targets.wheel]
packages = ["preprint_fulltext"]

[tool.pytest.ini_options]
minversion = "8.0"
testpaths = ["tests"]
addopts = "-ra --strict-markers"
markers = [
  "live: opt-in tests that hit the live network; skipped unless PREPRINT_FULLTEXT_LIVE=1",
  "live_s3: opt-in requester-pays S3 tests; skipped unless PREPRINT_FULLTEXT_LIVE_S3=1",
]

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