Metadata-Version: 2.1
Name: cellmaps_coembedding
Version: 0.1.0a5
Summary: A tool to generate coembeddings from IF image embeddings and PPI network embeddings
Home-page: https://github.com/idekerlab/cellmaps_coembedding
Author: Ideker Lab CM4AI team
Author-email: tools@cm4ai.org
License: MIT license
Description: =====================
        Cell Maps CoEmbedder
        =====================
        
        
        .. image:: https://img.shields.io/pypi/v/cellmaps_coembedding.svg
                :target: https://pypi.python.org/pypi/cellmaps_coembedding
        
        .. image:: https://img.shields.io/travis/idekerlab/cellmaps_coembedding.svg
                :target: https://travis-ci.com/idekerlab/cellmaps_coembedding
        
        .. image:: https://readthedocs.org/projects/cellmaps-generate-ppi/badge/?version=latest
                :target: https://cellmaps-generate-ppi.readthedocs.io/en/latest/?badge=latest
                :alt: Documentation Status
        
        Creates Coembedding from `Cell Maps ImmunoFluorscent Image Embedder <https://cellmaps-image-embedding.readthedocs.io>`__
        and `Cell Maps PPI Embedder <https://cellmaps-ppi-embedding.readthedocs.io>`__ for `Cell Maps for AI (CM4AI) <https://cm4ai.org>`__
        
        * Free software: MIT license
        * Documentation: https://cellmaps-coembedding.readthedocs.io.
        
        
        
        Dependencies
        ------------
        
        * `cellmaps_utils <https://pypi.org/project/cellmaps-utils>`__
        * `phenograph <https://pypi.org/project/phenograph>`__
        * `numpy <https://pypi.org/project/numpy>`__
        * `torch <https://pypi.org/project/torch>`__
        * `pandas <https://pypi.org/project/pandas>`__
        * `matplotlib <https://pypi.org/project/matplotlib>`__
        * `dill <https://pypi.org/project/dill>`__
        * `tqdm <https://pypi.org/project/tqdm>`__
        
        
        Compatibility
        -------------
        
        * Python 3.8+
        
        Installation
        ------------
        
        .. code-block::
        
           git clone https://github.com/idekerlab/cellmaps_coembedding
           cd cellmaps_coembedding
           make dist
           pip install dist/cellmaps_coembedding*whl
        
        
        Run **make** command with no arguments to see other build/deploy options including creation of Docker image 
        
        .. code-block::
        
           make
        
        Output:
        
        .. code-block::
        
           clean                remove all build, test, coverage and Python artifacts
           clean-build          remove build artifacts
           clean-pyc            remove Python file artifacts
           clean-test           remove test and coverage artifacts
           lint                 check style with flake8
           test                 run tests quickly with the default Python
           test-all             run tests on every Python version with tox
           coverage             check code coverage quickly with the default Python
           docs                 generate Sphinx HTML documentation, including API docs
           servedocs            compile the docs watching for changes
           testrelease          package and upload a TEST release
           release              package and upload a release
           dist                 builds source and wheel package
           install              install the package to the active Python's site-packages
           dockerbuild          build docker image and store in local repository
           dockerpush           push image to dockerhub
        
        For developers
        -------------------------------------------
        
        To deploy development versions of this package
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        Below are steps to make changes to this code base, deploy, and then run
        against those changes.
        
        #. Make changes
        
           Modify code in this repo as desired
        
        #. Build and deploy
        
        .. code-block::
        
            # From base directory of this repo cellmaps_coembedding
            pip uninstall cellmaps_coembedding -y ; make clean dist; pip install dist/cellmaps_coembedding*whl
        
        
        
        Needed files
        ------------
        
        **TODO:** Add description of needed files
        
        
        Usage
        -----
        
        For information invoke :code:`cellmaps_coembeddingcmd.py -h`
        
        **Example usage**
        
        **TODO:** Add information about example usage
        
        .. code-block::
        
           cellmaps_coembeddingcmd.py # TODO Add other needed arguments here
        
        
        Via Docker
        ~~~~~~~~~~~~~~~~~~~~~~
        
        **Example usage**
        
        **TODO:** Add information about example usage
        
        
        .. code-block::
        
           docker run -v `pwd`:`pwd` -w `pwd` idekerlab/cellmaps_coembedding:0.1.0 cellmaps_coembeddingcmd.py # TODO Add other needed arguments here
        
        
        Credits
        -------
        
        This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
        
        .. _Cookiecutter: https://github.com/audreyr/cookiecutter
        .. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
        .. _NDEx: http://www.ndexbio.org
        
        
        =======
        History
        =======
        
        0.1.0 (2023-05-19)
        ------------------
        
        * First release on PyPI.
        
Keywords: cellmaps_coembedding
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Description-Content-Type: text/x-rst
