=============================== Cell Maps Hierarchy Evaluation

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.. image:: https://readthedocs.org/projects/cellmaps-hierarchyeval/badge/?version=latest :target: https://cellmaps-hierarchyeval.readthedocs.io/en/latest/?badge=latest :alt: Documentation Status

evaluate hidef hierarchy

• Free software: MIT license
• Documentation: https://cellmaps-hierarchyeval.readthedocs.io.

Dependencies

• cellmaps_utils <https://pypi.org/project/cellmaps-utils>__
• statsmodels <https://pypi.org/project/statsmodels>__
• tqdm <https://pypi.org/project/tqdm>__
• scipy <https://pypi.org/project/scipy>__
• numpy <https://pypi.org/project/numpy>__
• ndex2 <https://pypi.org/project/ndex2>__

Compatibility

• Python 3.8+

Installation

.. code-block::

git clone https://github.com/idekerlab/cellmaps_hierarchyeval cd cellmaps_hierarchyeval make dist pip install dist/cellmaps_hierarchyevalcmd*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

Before running tests, please install: pip install -r requirements_dev.txt.

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_hierarchyeval
    pip uninstall cellmaps_hierarchyeval -y ; make clean dist; pip install dist/cellmaps_hierarchy*whl

Needed files
------------

**TODO:** Add description of needed files

Usage
-----

For information invoke :code:`cellmaps_hierarchyevalcmd.py -h`

**Example usage**

**TODO:** Add information about example usage

.. code-block::

   cellmaps_hierarchyevalcmd.py # TODO Add other needed arguments here

Via Docker

Example usage

TODO: Add information about 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