pyproject.toml

[tool.poetry]
name = "gen3"
homepage = "https://gen3.org/"
version = "5.0.0"
description = "Gen3 CLI and Python SDK"
authors = ["Center for Translational Data Science at the University of Chicago <support@gen3.org>"]
license = "Apache-2.0"
packages = [
    { include = "gen3" },
]
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "Intended Audience :: Developers",
    "License :: OSI Approved :: Apache Software License",
    "Programming Language :: Python :: 3.13",
    "Topic :: Scientific/Engineering",
]

[tool.poetry.dependencies]
python = ">=3.13, <4"
requests = "*"
httpx2 = ">=2.9.1"
indexclient = ">=2.3.0"
drsclient = ">=0.3.0"
aiohttp = "*"
backoff = "*"
cdislogging = ">=1.1.0"
click = "*"
importlib_metadata = ">=8,<9"
jsonschema = "*"
# FIXME updating to >=0.6.0 breaks a few tests
dataclasses-json = "<=0.5.9"
pypfb = ">=0.6.2"
tqdm = ">=4.61.2"
humanfriendly ="*"
python-dateutil = "*"
aiofiles = "*"
pandas = ">=1.4.2"
xmltodict = ">=0.13.0"
gen3users = "*"
joserfc = ">=1.7.3"

authutils = ">=9.0.0"

# A list of all of the optional dependencies, some of which are included in the
# below `extras`. They can be opted into by apps.
# fhir
fhirclient = { version = "*", optional = true }

# dpop
uvicorn = { version = "*", optional = true }

[tool.poetry.extras]
fhir = ["fhirclient"]
dpop = ["uvicorn"]

[tool.poetry.group.dev.dependencies]
pytest = ">=6.0.0"
pytest-cov = "*"
pytest-xdist = "*"
requests-mock = "*"
deptry = ">=0.23.1"

[tool.poetry.scripts]
gen3 = "gen3.cli.__main__:main"

[tool.poetry.plugins."gen3.plugins"]

[build-system]
requires = ["poetry>=1.4.1"]
build-backend = "poetry.masonry.api"

[tool.pytest.ini_options]
minversion = "6.0"
# Run tests in parallel (as much as possible) by default.
#
# `load`, xdist's default, hands each test to whichever worker is free, so two tests
# from the same module can run at once in different processes. `loadscope` instead
# groups tests by class, or by module for tests outside one, and gives each whole
# group to a single worker, so a module's tests stay in order in one process.
#
# `--dist loadscope` MUST accompany `-n`. Why? Some modules are not independent
# test-by-test:
#   - the fixed TMP_FOLDER in gen3/tools/indexing/download_manifest.py, which the
#     library wipes on entry and then collects with a glob
#   - the ~/.cache/gen3 token cache, keyed by API key rather than by test
#   - download_tests/test_resolvers.py, where one test reads a DRS cache file that an
#     earlier test in the module wrote
#   - others? there might be...
#
# Under `load` these corrupt each other or go missing, and which tests fail moves
# around from run to run. Thus, `loadscope` keeps things safe.
#
# Pass `-n0` to run serially if needed for debugging.
addopts = "-vv --dist loadscope -n auto"
testpaths = [
    "tests",
]