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pyproject.toml
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pyproject.toml
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[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"
[project]
name = "vitessce"
version = "3.5.0"
authors = [
{ name="Mark Keller", email="[email protected]" },
]
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 = [
'zarr>=2.5.0',
'numcodecs>=0.5.7',
'scipy>=1.2.1',
'negspy>=0.2.24',
'pandas>=1.1.2',
'black>=21.11b1',
'numpy>=1.21.2',
'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>=0.8.3',
'tifffile>=2020.10.1',
'jsonschema>=3.2',
'tqdm>=4.1.0'
]
[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==5.6.1',
'jinja2==3.0.3',
]
all = [
'jupyter-server-proxy>=1.5.2',
'esbuild_py>=0.1.3',
'anywidget>=0.9.10',
'uvicorn>=0.17.0',
'ujson>=4.0.1',
'starlette==0.14.0',
'generate-tiff-offsets>=0.1.8',
'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 = []
demos = [
"pulp==2.7.0",
"snakemake",
"pyyaml",
]
[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',
]
[tool.uv]
default-groups = ["dev"]
override-dependencies = [
'starlette==0.14.0'
]
[tool.hatch.build]
exclude = [".github", "docs", "demos", "binder"]
[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"]