cellmaps-generate-hierarchy 0.2.5
A tool to generate hierarchies from protein to protein interaction networks
License: MIT license
Keywords: cellmaps_generate_hierarchy

=============================
Cell Maps Generate Hierarchy
=============================
The Cell Maps Generate Hierarchy is part of the Cell Mapping Toolkit

.. image:: https://img.shields.io/pypi/v/cellmaps_generate_hierarchy.svg
        :target: https://pypi.python.org/pypi/cellmaps_generate_hierarchy

.. image:: https://app.travis-ci.com/idekerlab/cellmaps_generate_hierarchy.svg?branch=main
        :target: https://app.travis-ci.com/github/idekerlab/cellmaps_generate_hierarchy

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

Generates hierarchy from `Cell Maps Coembedding <https://cellmaps-coembedding.readthedocs.io/>`__ using `HiDeF <https://github.com/fanzheng10/HiDeF/>`__

* Free software: MIT license
* Documentation: https://cellmaps-generate-hierarchy.readthedocs.io.
* Source code: https://github.com/idekerlab/cellmaps_generate_hierarchy

Dependencies
------------

* `cellmaps_utils <https://pypi.org/project/cellmaps-utils>`__
* `tqdm <https://pypi.org/project/tqdm>`__
* `pandas <https://pypi.org/project/pandas>`__
* `numpy <https://pypi.org/project/numpy>`__
* `ndex2 <https://pypi.org/project/ndex2>`__
* `HiDeF <https://pypi.org/project/hidef>`__

Compatibility
-------------

* Python 3.8 - 3.11

Installation
------------

.. code-block::

   git clone https://github.com/idekerlab/cellmaps_generate_hierarchy
   cd cellmaps_generate_hierarchy
   pip install -r requirements_dev.txt
   make dist
   pip install dist/cellmaps_generate_hierarchy*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_generate_hierarchy
    pip uninstall cellmaps_generate_hierarchy -y ; make clean dist; pip install dist/cellmaps_generate_hierarchy*whl



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

The output directory for co-embedding is required (see `Cell Maps Coembedding <https://github.com/idekerlab/cellmaps_coembedding/>`__).

Usage
-----

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

**Example usage**

.. code-block::

   cellmaps_generate_hierarchycmd.py ./cellmaps_generate_hierarchy --coembedding_dirs ./cellmaps_coembedding_outdir

Via Docker
~~~~~~~~~~~~~~~~~~~~~~

**Example usage**


.. code-block::

   Coming soon...

Cite
-------

If you find this tool useful, please cite:

Lenkiewicz, J., Churas, C., Hu, M., Qian, G., Jain, M., Levinson, M. A., ... & Schaffer, L. V. (2025). Cell Mapping Toolkit: An end-to-end pipeline for mapping subcellular organization. Bioinformatics, 41(6), btaf205.

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
=======

0.2.5 (2025-10-08)
-------------------

* Remove leading spaces from name of hierarchy.

0.2.4 (2025-05-15)
-------------------

* Updated to PEP 517 compliant build system

0.2.3 (2025-03-19)
------------------

* Update requirements versions

* Increase timeout for cmd run

* Fix 'k' argument type

0.2.2 (2024-11-25)
------------------

* Added default argument for password.

0.2.1 (2024-11-08)
------------------

* Fixed types of arguments.


0.2.0 (2024-10-16)
------------------

* Added the ``--bootstrap_edges`` flag, which allows specifying the percentage of edges to be randomly removed
  from each PPI network (across networks at different PPI cutoffs).

* Added a style for proteins specified as bait.

* Refactored code and expose more methods for hierarchy generation from edgelists.


0.1.0 (2024-09-06)
------------------

* First release on PyPI.