pyproject.toml

[project]
name = "prepare-annotations"
version = "0.1.1"
description = "Add your description here"
readme = "README.md"
authors = [
    { name = "antonkulaga", email = "antonkulaga@gmail.com" }
]
requires-python = ">=3.13"
dependencies = [
    "aiohttp>=3.13.2",
    "dagster>=1.12.10",
    "dagster-polars>=0.27.8",
    "dagster-webserver>=1.12.10",
    "duckdb>=1.4.3",
    "eliot>=1.17.5",
    "fsspec>=2025.12.0",
    "graphviz>=0.21",
    "huggingface-hub>=1.2.3",
    "polars>=1.36.1",
    "polars-bio>=0.19.0",
    "pooch>=1.8.2",
    "psutil>=7.1.3",
    "pycomfort>=0.0.18",
    "pydantic>=2.12.5",
    "pyfaidx>=0.9.0.3",
    "pyyaml>=6.0.3",
    "requests>=2.32.5",
    "rich>=14.2.0",
    "s3fs>=2025.12.0",
    "tenacity>=9.1.2",
    "typer>=0.19.2",
]

[project.scripts]
prepare-annotations = "prepare_annotations.cli:app"
prepare = "prepare_annotations.cli:dagster_app"
modules = "prepare_annotations.converters.modules:app"
dagster-ensembl = "prepare_annotations.cli:_run_ensembl_cli"
dagster-ui = "prepare_annotations.cli:_run_ui_cli"

[build-system]
requires = ["uv-build"]
build-backend = "uv_build"

[dependency-groups]
dev = [
    "cyvcf2>=0.31.4",
    "jupyterlab>=4.5.1",
    "marimo>=0.18.4",
    "pytest>=9.0.2",
]

[tool.pytest.ini_options]
markers = [
    "large_download: marks tests that download large files (multi-GB) - skip by default",
    "integration: marks integration tests that require network access",
    "slow: marks tests that take a long time to run"
]

# Default pytest behavior: extra verbose and no capture to allow Eliot/stdout output
addopts = "-vvv -s -m 'not large_download'"
testpaths = ["tests"]
filterwarnings = [
    "ignore::DeprecationWarning:eliottree.*",
    "ignore:datetime.datetime.utcfromtimestamp\\(\\) is deprecated:DeprecationWarning",
]