pyproject.toml

[build-system]
requires = ["setuptools"]

[project]
name = "scholarag"
authors = [
    {name = "Blue Brain Project, EPFL"},
]
description = "Pipelines for RAG on scientific papers"
readme = "README.md"
requires-python = ">=3.10"
dynamic = ["version"]
dependencies = [
    "aiobotocore",
    "asgi-correlation-id",
    "boto3",
    "cohere",
    "elasticsearch >= 8.5",
    "elasticsearch-dsl",
    "fastapi <= 0.112.0",
    "fastapi-pagination",
    "httpx",
    "python-dotenv",
    "openai",
    "openpyxl",
    "opensearch-py >= 2.5.0",
    "pandas",
    "pydantic",
    "pydantic-settings",
    "redis",
    "sentry-sdk[fastapi]",
    "types-redis",
    "uvicorn",
]

[project.optional-dependencies]
dev = [
    "bandit[toml]",
    "moto[server]",
    "mypy",
    "pytest",
    "pytest-cov",
    "pytest_asyncio",
    "pytest_httpx",
    "ruff",
    "types-requests",
    ]
doc = ["mkdocs", "mkdocs-material", "mkdocstrings[python]"]

[project.scripts]
create-impact-factors-index = "scholarag.scripts.create_impact_factor_index:main"
manage-index = "scholarag.scripts.manage_index:main"
parse-and-upload = "scholarag.scripts.parse_and_upload:main"
pu-consumer = "scholarag.scripts.pu_consumer:main"
pu-producer = "scholarag.scripts.pu_producer:main"
pmc-parse-and-upload = "scholarag.scripts.pmc_parse_and_upload:main"
scholarag-api = "scholarag.scripts.scholarag_api:main"

[tool.setuptools.dynamic]
version = {attr = "scholarag.__version__"}

[tool.setuptools.packages.find]
where = ["src"]
namespaces = false

[tool.bandit]
exclude_dirs = ["tests"]

[tool.ruff]
line-length = 88
target-version = "py310"

[tool.ruff.lint]
select = ["E4", "E7", "E9", "F", "I", "D"]

[tool.ruff.lint.pydocstyle]
convention = "numpy"

[tool.ruff.lint.per-file-ignores]
"tests/*" = ["D"]

[tool.mypy]
mypy_path = "src"
python_version = "3.10"
ignore_missing_imports = true
no_implicit_optional = true
check_untyped_defs = true
strict_equality = true
warn_redundant_casts = true
warn_unused_ignores = true
show_error_codes = true
disallow_any_generics = true
disallow_incomplete_defs = true
disallow_untyped_defs = true
plugins = [
  "pydantic.mypy"
]

[tool.pytest.ini_options]
asyncio_mode = "auto"
minversion = "6.0"
testpaths = [
    "tests",
]
filterwarnings = [
    "error",
    "ignore:Exception ignored in:pytest.PytestUnraisableExceptionWarning",
    "ignore:sentry_sdk.configure_scope is deprecated and will be removed in the next major version:DeprecationWarning",
    "ignore:Support for class-based `config` is deprecated, use ConfigDict instead.:pydantic.warnings.PydanticDeprecatedSince20",
    "ignore:Valid config keys have changed in V2:UserWarning",
    "ignore:`json_encoders` is deprecated:pydantic.warnings.PydanticDeprecatedSince20"
]
markers = [
    "slow: marks tests as slow",
]
addopts = "--cov=src/ --cov=tests/ -v --cov-report=term-missing --durations=20 --no-cov-on-fail"