pyproject.toml

[build-system]
build-backend = "hatchling.build"
requires = ["hatchling", "hatch-vcs"]


[project]
name = "spatialdata-io"
dynamic= [
  "version" # allow version to be set by git tags
]
description = "SpatialData IO for common techs"
readme = "README.md"
requires-python = ">=3.9"
license = {file = "LICENSE"}
authors = [
    {name = "scverse"},
]
maintainers = [
    {name = "scverse", email = "scverse@scverse.scverse"},
]
urls.Documentation = "https://spatialdata-io.readthedocs.io/"
urls.Source = "https://github.com/scverse/spatialdata-io"
urls.Home-page = "https://github.com/scverse/spatialdata-io"
dependencies = [
    "anndata",
    "numpy",
    "scanpy",
    "spatialdata>=0.2.3",
    "scikit-image",
    "h5py",
    "joblib",
    "imagecodecs",
    "dask-image",
    "pyarrow",
    "readfcs",
    "tifffile>=2023.8.12",
]

[project.optional-dependencies]
dev = [
    # CLI for bumping the version number
    "bump2version",
    "pre-commit"
]
doc = [
    "sphinx>=4.5",
    "sphinx-book-theme>=1.0.0",
    "myst-nb",
    "sphinxcontrib-bibtex>=1.0.0",
    "sphinx-autodoc-typehints",
    "sphinx-design",
    # For notebooks
    "ipython>=8.6.0",
    "sphinx-copybutton",
]
test = [
    "pytest",
    "pytest-cov",
]
# this will be used by readthedocs and will make pip also look for pre-releases, generally installing the latest available version
pre = [
    "spatialdata>=0.1.0-pre0"
]

[tool.coverage.run]
source = ["spatialdata_io"]
omit = [
    "**/test_*.py",
]

[tool.pytest.ini_options]
testpaths = ["tests"]
xfail_strict = true
addopts = [
    "--import-mode=importlib",  # allow using test files with same name
]

[tool.isort]
include_trailing_comma = true
multi_line_output = 3
profile = "black"
skip_glob = ["docs/*"]

[tool.black]
line-length = 120
target-version = ['py39']
include = '\.pyi?$'
exclude = '''
(
  /(
      \.eggs
    | \.git
    | \.hg
    | \.mypy_cache
    | \.tox
    | \.venv
    | _build
    | buck-out
    | build
    | dist
  )/
)
'''

[tool.jupytext]
formats = "ipynb,md"

[tool.hatch.metadata]
allow-direct-references = true

[tool.hatch.build.targets.wheel]
packages = ['src/spatialdata_io']

[tool.hatch.version]
source = "vcs"

[tool.hatch.build.hooks.vcs]
version-file = "_version.py"