pyproject.toml

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

[project]
name = "vitessce"
version = "3.8.3"
authors = [
  { name="Mark Keller", email="mark_keller@hms.harvard.edu" },
]
description = "Jupyter widget facilitating interactive visualization of spatial single-cell data with Vitessce"
readme = "README.md"
license = {file = "LICENSE"}
requires-python = ">=3.10"
keywords = ["ipython", "jupyter", "widgets"]
classifiers = [
  'Development Status :: 4 - Beta',
  'Framework :: IPython',
  'Intended Audience :: Developers',
  'Intended Audience :: Science/Research',
  'Topic :: Multimedia :: Graphics',
  'Programming Language :: Python :: 3.9',
  'Programming Language :: Python :: 3.10',
  'Programming Language :: Python :: 3.11',
  'Programming Language :: Python :: 3.12',
]
dependencies = [
  'scipy>=1.2.1',
  'pandas>=1.1.2',
  'black>=21.11b1',
  'numpy>=1.21.2',
  'zarr>=2.5.0,<3',
  'numcodecs>=0.5.7,<0.16.0',
]

[project.optional-dependencies]
dev = []
docs = [
  'sphinx==4.2.0',
  'sphinx-rtd-theme==1.0.0',
  
  # Pin sub-dependencies of sphinx
  # Reference: https://github.com/sphinx-doc/sphinx/issues/11130
  'sphinxcontrib-applehelp==1.0.4',
  'sphinxcontrib-devhelp==1.0.2',
  'sphinxcontrib-htmlhelp==2.0.1',
  'sphinxcontrib-jsmath==1.0.1',
  'sphinxcontrib-qthelp==1.0.3',
  'sphinxcontrib-serializinghtml==1.1.5',
  
  'nbsphinx==0.8.8',
  'nbclean==0.3.2',
  # Pin sqlalchemy to before 1.4 to fix issue importing nbclean.NotebookCleaner
  # Reference: https://docs.sqlalchemy.org/en/14/core/sqlelement.html#sqlalchemy.sql.expression.case.params.*whens
  'sqlalchemy==1.3.24',
  # nbconvert and jinja2 versions need to be pinned.
  # Reference: https://github.com/vitessce/vitessce-python/issues/152
  'nbconvert>=6.2',
  'jinja2',
]
all = [
  # For data_utils
  'negspy>=0.2.24',
  'anndata>=0.7.8',
  # scanpy < 1.10.3 does not support numpy >= 2.0.0 and does not
  # Reference: https://github.com/scverse/scanpy/pull/3115/files
  'scanpy>=1.10.2',
  'ome-zarr<0.10.3',
  'tifffile>=2020.10.1',

  'jupyter-server-proxy>=1.5.2',
  'oxc-py>=0.1.1',
  'anywidget>=0.9.10',
  'uvicorn>=0.17.0',
  'ujson>=4.0.1',
  'starlette>=0.14.0',
  'generate-tiff-offsets>=0.1.9',
  'kerchunk>=0.2.6',
  'fsspec',

  # aiofiles is not explicitly referenced in our code,
  # but it is an implicit dependency of starlette==0.14.0.
  # https://github.com/encode/starlette/issues/49
  # Upgrading starlette will remove this dependency.
  'aiofiles>=0.6.0'
]
building = []
testing = []
linting = []
notebook = [
  'spatialdata>=0.3.0',
  'dask[dataframe]==2024.11.1',
  'marimo',
  'starlette>=0.42.0',
  'tqdm>=4.1.0',
]
demos = [
  "pulp==2.7.0",
  "snakemake",
  "pyyaml",
]
# SpatialQuery
sq = [
  # When installing with `uv`, may need --no-build-isolation-package SpatialQuery
  "pybind11",
  # As of writing, `main` reflects SpatialQuery commit 9dde563 (April 4, 2026).
  "SpatialQuery==0.0.4"
]

[dependency-groups]
dev = [
  'build==0.1.0',
  'pytest>=6.2.4',
  'loompy>=3.0.6',
  'coverage>=6.3.2',
  'flake8>=3.8.4',
  #'spatialdata>=0.2.2',
  'jupyterlab',
  'numba>=0.53.0',
  'jupyterlab>=3',
  'boto3>=1.16.30',
  'scikit-misc>=0.1.3',
  'autopep8>=2.0.2',
  'spatialdata>=0.3.0',
  'dask[dataframe]==2024.11.1',
]

[tool.uv]
default-groups = ["dev"]
override-dependencies = []

[tool.hatch.build]
exclude = [".github", "docs", "demos", "binder"]

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

[project.urls]
repository = "https://github.com/vitessce/vitessce-python"

[tool.setuptools]
packages = ["vitessce", "vitessce.data_utils", "vitessce.widget_plugins"]
package-dir = {"" = "src"}

# Reference: https://stackoverflow.com/a/50156706
[tool.pytest.ini_options]
pythonpath = ["src"]
testpaths = ["tests"]
addopts = ["--doctest-modules", "--verbose", "--ignore=docs", "--ignore=demos"]