Metadata-Version: 2.1
Name: cellmaps-pipeline
Version: 0.1.0a17
Summary: Runs full Cell Maps pipeline
Home-page: https://github.com/idekerlab/cellmaps_pipeline
Author: Ideker Lab Cell Maps team
Author-email: tools@cm4ai.org
License: MIT license
Description: ===================
        Cell Maps Pipeline
        ===================
        
        
        .. image:: https://img.shields.io/pypi/v/cellmaps_pipeline.svg
                :target: https://pypi.python.org/pypi/cellmaps_pipeline
        
        .. image:: https://app.travis-ci.com/idekerlab/cellmaps_pipeline.svg?branch=main
                :target: https://app.travis-ci.com/idekerlab/cellmaps_pipeline
        
        .. image:: https://readthedocs.org/projects/cellmaps-pipeline/badge/?version=latest
                :target: https://cellmaps-pipeline.readthedocs.io/en/latest/?badge=latest
                :alt: Documentation Status
        
        * Free software: MIT license
        * Documentation: https://cellmaps-pipeline.readthedocs.io.
        
        Dependencies
        ------------
        
        * `cellmaps_utils <https://pypi.org/project/cellmaps-utils>`__
        * `cellmaps_imagedownloader <https://pypi.org/project/cellmaps-imagedownloader>`__
        * `cellmaps_ppidownloader <https://pypi.org/project/cellmaps-ppidownloader>`__
        * `cellmaps_image_embedding <https://pypi.org/project/cellmaps-image-embedding>`__
        * `cellmaps_ppi_embedding <https://pypi.org/project/cellmaps-ppi-embedding/>`__
        * `cellmaps_coembedding <https://pypi.org/project/cellmaps-coembedding>`__
        * `cellmaps_generate_hierarchy <https://pypi.org/project/cellmaps-generate-hierarchy>`__
        * `networkx <https://pypi.org/project/networkx>`__
        
        Compatibility
        -------------
        
        * Python 3.8+
        
        Installation
        ------------
        
        .. code-block::
        
           git clone https://github.com/idekerlab/cellmaps_pipeline
           cd cellmaps_pipeline
           make dist
           pip install dist/cellmaps_pipeline*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_pipeline
            pip uninstall cellmaps_pipeline -y ; make clean dist; pip install dist/cellmaps_pipeline*whl
        
        
        
        Needed files
        ------------
        
        * samples file: CSV file with list of IF images to download (see sample samples file in examples folder)
        * unique file: CSV file of unique samples (see sample unique file in examples folder)
        * bait list file: TSV file of baits used for AP-MS experiments
        * edge list file: TSV file of edges for protein interaction network
        * provenance: file containing provenance information about input files in JSON format (see sample provenance file in examples folder)
        
        Usage
        -----
        
        For information invoke :code:`cellmaps_pipelinecmd.py -h`
        
        **Example usage**
        
        .. code-block::
        
           cellmaps_pipelinecmd.py ./cellmaps_pipeline_outdir --samples examples/samples.csv --unique examples/unique.csv --edgelist examples/edgelist.tsv --baitlist examples/baitlist.tsv --provenance examples/provenance.json
        
        
        Via Docker
        ~~~~~~~~~~~~~~~~~~~~~~
        
        **Example usage**
        
        
        .. code-block::
        
           Coming soon...
        
        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 (2023-05-22)
        ------------------
        
        * First release on PyPI.
        
Keywords: cellmaps_pipeline
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
