mirror of
https://github.com/chanzuckerberg/cellxgene.git
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907cc634f5
This PR contains a refactoring to make adding new features easier. The new features include supporting the tiledb format, and the multi dataset application. The refactoring includes Simplifying the directory structure and files. a class structure to handle annotations (currently one type: AnnotationsLocalFile). a class to handle application configuration a class structure to handle matrix data (currently AnndataAdaptor and CxgAdaptor). CxgAdaptor uses tiledb. Algorithms that were previously dependent on the scanpy anndata object are now generalized to work with an abstract interface. The multi dataset option is not fully supported yet, and so the option to use it is hidden. Use "cli launch --dataroot ..." To access this feature. All combinations of app single dataset/ app multi dataset and AnndataAdaptor/CxgAdaptor work with all the features, such as annotations, ontologies, diffexp.
44 lines
1.5 KiB
Python
44 lines
1.5 KiB
Python
from setuptools import setup, find_packages
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with open("README.md", "rb") as fh:
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long_description = fh.read().decode()
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with open("server/requirements.txt") as fh:
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requirements = fh.read().splitlines()
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with open("server/requirements-prepare.txt") as fh:
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requirements_prepare = fh.read().splitlines()
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setup(
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name="cellxgene",
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version="0.14.0",
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packages=find_packages(),
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url="https://github.com/chanzuckerberg/cellxgene",
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license="MIT",
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author="Chan Zuckerberg Initiative",
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author_email="cellxgene@chanzuckerberg.com",
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description="Web application for exploration of large scale scRNA-seq datasets",
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long_description=long_description,
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long_description_content_type="text/markdown",
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install_requires=requirements,
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include_package_data=True,
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zip_safe=False,
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classifiers=[
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"Framework :: Flask",
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"Intended Audience :: Science/Research",
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"License :: OSI Approved :: MIT License",
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"Natural Language :: English",
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"Operating System :: POSIX",
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"Operating System :: Unix",
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"Operating System :: MacOS :: MacOS X",
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"Programming Language :: JavaScript",
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"Programming Language :: Python :: 3",
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"Programming Language :: Python :: 3.6",
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"Programming Language :: Python :: 3.7",
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"Programming Language :: Python :: 3 :: Only",
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"Topic :: Scientific/Engineering :: Bio-Informatics",
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],
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entry_points={"console_scripts": ["cellxgene = server.cli.cli:cli"]},
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extras_require=dict(prepare=requirements_prepare),
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)
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