Metadata-Version: 2.1
Name: nufeb_tools
Version: 0.1.11
Summary: Python-based tools and utilities for NUFEB simulations
Home-page: https://github.com/Jsakkos/nufeb-tools
Author: Jonathan Sakkos
Author-email: sakkosjo@msu.edu
License: MIT
Project-URL: Documentation, https://nufeb-tools.readthedocs.io/en/latest/
Project-URL: Source, https://github.com/Jsakkos/nufeb_tools/nufeb_tools
Project-URL: Tracker, https://github.com/Jsakkos/nufeb_tools/issues
Project-URL: Download, https://pypi.org/project/nufeb-tools/#files
Platform: any
Classifier: Development Status :: 3 - Alpha
Classifier: Programming Language :: Python
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering
Description-Content-Type: text/x-rst; charset=UTF-8
Provides-Extra: testing
License-File: LICENSE.txt
License-File: AUTHORS.rst

===========
nufeb_tools
===========

|docs|  |pypi|  |tests|  |DOI|




Description
===========

Python-based tools and utilities for NUFEB simulations 

Getting Started
===============

Install via pip::

        pip install nufeb-tools

Generate NUFEB simulations from the CLI::

        nufeb-seed

Remove old runs::

        nufeb-clean

Get data from a simulation for analysis

.. code-block:: python

    from nufeb_tools import utils
    x = utils.get_data(test=True)

Plot the overall growth

.. code-block:: python

    from nufeb_tools import plot
    import matplotlib.pyplot as plt
    f, ax = plt.subplots()
    plot.overall_growth(x.biomass,ax=ax)

.. image:: /docs/_static/images/total_biomass_vs_time.png
   :align: center

Plot colonies based on initial seed cells

.. code-block:: python

    from nufeb_tools import utils, plot
    import matplotlib.pyplot as plt
    x = utils.get_data(directory=r'E:\sucrose\runs\Run_50_50_1.00e+00_1_2022-01-11_48525')
    f,ax = plt.subplots()
    plot.colony(x,25900,colors,ax=ax)
    plt.show()

.. image:: /docs/_static/images/colonies.png
   :align: center



.. |docs| image:: https://readthedocs.org/projects/nufeb-tools/badge/?version=latest
        :target: https://nufeb-tools.readthedocs.io/en/latest/?badge=latest
        :alt: Documentation Status

.. |pypi| image:: https://badge.fury.io/py/nufeb-tools.svg
        :target: https://badge.fury.io/py/nufeb-tools

.. |tests| image:: https://github.com/Jsakkos/nufeb-tools/actions/workflows/Test.yml/badge.svg
        :alt: Tox testing status


.. |DOI| image:: https://zenodo.org/badge/372038007.svg
        :target: https://zenodo.org/badge/latestdoi/372038007


