aind-zarr-utils/pyproject.toml at main · AllenNeuralDynamics/aind-zarr-utils · GitHub

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

[project]
name = "aind-zarr-utils"
description = "Utilities for working with ZARR data and AIND metadata"
license = "MIT"
requires-python = ">=3.10"
authors = [
  { name = "Allen Institute for Neural Dynamics" },
  { name = "Galen Lynch", email = "galen@galenlynch.com" },
]
classifiers = ["Programming Language :: Python :: 3"]
readme = "README.md"
version = "0.14.1"

dependencies = [
  "aind-anatomical-utils>=0.4",
  "aind-registration-utils>=0.1",
  "aind-s3-cache>=0.1",
  "antspyx>=0.2",
  # boto3
  # Package depends on boto3, but ome-zarr requires s3fs and this causes
  # pip dependency resolution issues if specified here.
  "numpy>=2",
  "ome-zarr>=0.7",
  "requests>=2",
  # This is a workaround for pip dependency problems with ome-zarr: s3fs is
  # NOT a direct dependency of this package, but ome-zarr requires it.
  # boto3 option required to help pip resolve dependencies
  "s3fs>=2021",
  "SimpleITK>=2",
]

[project.urls]
Repository = "https://github.com/AllenNeuralDynamics/aind-zarr-utils/"
Issues = "https://github.com/AllenNeuralDynamics/aind-zarr-utils/issues"
Changelog = "https://github.com/AllenNeuralDynamics/aind-zarr-utils/blob/main/CHANGELOG.md"

[dependency-groups]
types = ["mypy", "types-requests", "boto3-stubs[s3]"]
dev = [{ include-group = "types" }, "codespell", "pytest", "pytest-cov", "ruff", "interrogate"]
jupyter = [{ include-group = "dev" }, "ipykernel", "pip"]
docs = [
  { include-group = "dev" },
  "sphinx>=5.0",
  "sphinx-autodoc-typehints",
  "sphinx-copybutton",
  "myst-parser",
  "nbsphinx",
  "furo",
]

[tool.hatch.build.targets.wheel]
packages = ["src/aind_zarr_utils"]

[tool.ruff]
line-length = 120
target-version = "py310"
extend-exclude = ["scratch", "docs/build", "docs/source/api-reference/generated"]

[tool.ruff.lint]
extend-select = ["Q", "RUF100", "C90", "I", "F", "E", "W", "D", "UP", "ANN", "PYI"]
extend-ignore = ["ANN401"]  # Skip self/cls type annotations
per-file-ignores = { "tests/*.py" = ["ANN", "D"] }
mccabe = { max-complexity = 14 }
pydocstyle = { convention = "numpy" }

[tool.codespell]
skip = ".git,*.pdf,*.svg,./docs/build,./docs/_build,uv.lock,scratch,*searchindex.js"
ignore-words-list = "nd"

[tool.pytest.ini_options]
addopts = "--strict-markers --tb=short --cov=src --cov-report=term-missing --cov-fail-under=0"
testpaths = ["tests"]

[tool.interrogate]
ignore-init-method = true
ignore-magic = true
ignore_module = true
fail-under = 30
exclude = [
  "__init__.py",
  "tests",
  "docs",
  "build",
  "examples",
  "site",
  "scratch",
  ".venv",
]

[tool.commitizen]
version_provider = "pep621"
update_changelog_on_bump = true
tag_format = "v$version"
major_version_zero = true


[tool.mypy]
files = ["src/aind_zarr_utils"]
python_version = "3.10"
warn_return_any = true
warn_unused_configs = true
disallow_untyped_defs = true
disallow_incomplete_defs = true
check_untyped_defs = true
disallow_untyped_decorators = true
no_implicit_optional = true
warn_redundant_casts = true
warn_unused_ignores = true
warn_no_return = true
warn_unreachable = true
strict_equality = true
show_error_codes = true
exclude = ["scratch"]

[[tool.mypy.overrides]]
module = "tests.*"
disallow_untyped_defs = false
disallow_incomplete_defs = false