pyproject.toml

[build-system]
requires = ["setuptools", "setuptools-scm"]
build-backend = "setuptools.build_meta"

[project]
# NOTE(hadim): unfortunately, we cannot use `polaris` on pypi.
# See https://github.com/pypi/support/issues/2908
name = "polaris-lib"
description = "Client for the Polaris Hub."
dynamic = ["version"]
authors = [
    { name = "Cas Wognum", email = "cas@valencelabs.com" },
    { name = "Lu Zhu", email = "lu@valencelabs.com" },
    { name = "Andrew Quirke", email = "andrew@valencelabs.com" },
    { name = "Julien St-Laurent", email = "julien.stl@valencelabs.com" },
]
readme = "README.md"
requires-python = ">=3.10,<3.13"
classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Intended Audience :: Developers",
    "Intended Audience :: Healthcare Industry",
    "Intended Audience :: Science/Research",
    "Topic :: Scientific/Engineering :: Artificial Intelligence",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Scientific/Engineering :: Information Analysis",
    "Topic :: Scientific/Engineering :: Medical Science Apps.",
    "Natural Language :: English",
    "Operating System :: OS Independent",
    "Programming Language :: Python",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
]
dependencies = [
    "authlib",
    "boto3 <1.36.0",
    "datamol >=0.12.1",
    "fastpdb",
    "fsspec[http]",
    "httpx",
    "numcodecs[msgpack] >=0.13.1, <0.16.0",
    "numpy <3",
    "pandas",
    "pyarrow < 18",
    "pydantic >=2",
    "pydantic-settings >=2",
    "pyroaring",
    "pyyaml",
    "rich>=13.9.4",
    "scikit-learn",
    "scipy",
    "seaborn",
    "typer",
    "typing-extensions>=4.12.0",
    "zarr >=2,<3",
]

[dependency-groups]
dev = [
    "ipywidgets",
    "jupyterlab",
    "moto[s3]>=5.0.14",
    "pytest >=7",
    "pytest-xdist",
    "pytest-cov",
    "ruff",
]
doc = [
    "mkdocs",
    "mkdocs-material >=9.4.7",
    "mkdocstrings",
    "mkdocstrings-python",
    "mkdocs-jupyter",
    "markdown-include",
    "mdx_truly_sane_lists",
    "mike >=1.0.0",
    "nbconvert",
]
codecs = [
    "imagecodecs",
]

# PEP 735 Dependency Groups are not well-supported by pip.
# Duplicate them here with the older syntax.
[project.optional-dependencies]
dev = [
    "ipywidgets",
    "jupyterlab",
    "moto[s3]>=5.0.14",
    "pytest >=7",
    "pytest-xdist",
    "pytest-cov",
    "ruff",
]
doc = [
    "mkdocs",
    "mkdocs-material >=9.4.7",
    "mkdocstrings",
    "mkdocstrings-python",
    "mkdocs-jupyter",
    "markdown-include",
    "mdx_truly_sane_lists",
    "mike >=1.0.0",
    "nbconvert",
]
codecs = [
    "imagecodecs",
]

[project.scripts]
polaris = "polaris.cli:app"

[project.urls]
Website = "https://polarishub.io/"
"Source Code" = "https://github.com/polaris-hub/polaris"
"Bug Tracker" = "https://github.com/polaris-hub/polaris/issues"
Documentation = "https://polaris-hub.github.io/polaris/"

[tool.setuptools]
include-package-data = true

[tool.setuptools_scm]
fallback_version = "0.0.0.dev1"

[tool.setuptools.packages.find]
where = ["."]
include = ["polaris", "polaris.*"]
exclude = []
namespaces = false

[tool.pytest.ini_options]
minversion = "7.0"
addopts = "--verbose --durations=10 -n auto --cov=polaris --cov-fail-under=75 --cov-report xml --cov-report term-missing"
testpaths = ["tests"]
pythonpath = "."
filterwarnings = ["ignore::DeprecationWarning:jupyter_client.connect.*:"]

[tool.coverage.run]
source = ["polaris/"]
disable_warnings = ["no-data-collected"]
data_file = ".coverage/coverage"

[tool.coverage.report]
omit = [
    "polaris/__init__.py",
    "polaris/_version.py",
    # We cannot yet test the interaction with the Hub.
    # See e.g. https://github.com/polaris-hub/polaris/issues/30
    "polaris/hub/client.py",
    "polaris/hub/external_client.py",
    "polaris/hub/settings.py",
    "polaris/hub/oauth.py",
    "polaris/hub/storage.py",
    "polaris/hub/__init__.py",
]

[tool.coverage.xml]
output = "coverage.xml"

[tool.ruff]
lint.ignore = [
    "E501", # Never enforce `E501` (line length violations).
]

lint.per-file-ignores."__init__.py" = [
    "F401", # imported but unused
    "E402", # Module level import not at top of file
]
line-length = 110
target-version = "py310"
extend-exclude = ["*.ipynb"]